The protagonist of "XBlaze Code: Embryo." Although he has a gentle personality, is brimming with curiosity, and seems very ordinary, he also has a strange side: once he sees a fight, he can't help but try to stop it. 
13 years before the Embryo Incident, the original Touya Kagari was brought to the Wadatsumi Research Laboratory by his mother, Ryouko Kagari, for a treatment for developing a Drive. He was an Irregular-Type Union who was infected before the Wadatsumi Incident and did not suffer the usual mental degradation, remaining in phase zero. Touya's Drive let him manipulate his blood, but because he was too young to endure his power, his blood degraded. His mother introduced him to Hinata Himezuru in the hope of giving her some happiness. The two became close friends. Touya tried to help Hinata escape from the Wadatsumi Research Facility, but his body started to break down after he used his Drive to protect her. Touya died at the age of 6.
After Ryouko Kagari shut down the T-System, Hinata used the power of the Embryo to wish for her friend's return. As a result, after the black tornado absorbed three thousand souls, it transformed the Origin of the Grimoire into a clone of Touya. This clone grew up in the same orphanage as Hinata and Yuki Himezuru until he was taken in by Yuki after she became a doctor.
Code: Embryo, Lost: Memories
After having a strange dream where he saw a girl with glowing blue eyes and heard his mother, Ryouko Kagari, tell him to “protect,” Touya woke up in his classroom to Hinata Himezuru's humming. He realized that it was already past four, and Akira Kamewari was running late. Akira arrived and returned a USB drive containing a summary of the serial killer reports that Touya had put together. Touya began to read an article about the Wadatsumi Incident on his phone, prompting Akira to steal his phone to look at it, telling Touya not to worry about the past. Touya then left to go to his part-time job at Maha Raja.
After getting out of work, Touya heard a strange bell-like sound and felt the urge to track it down. He followed the sound into the Restricted Ward. When Touya arrived, he found an injured Goro Joizumi, who tried to tell Touya to stay away from him. However, Goro succumbed to madness and began to see Touya as an enemy, attacking Touya with his Drive. Touya tried to run away but was eventually cornered. Before Goro could kill him, Es arrived and attacked Goro. Touya watched in horror as Es proceeded to mercilessly beat Goro down. Eventually, Touya jumped in the way to stop Es from killing Goro, but was knocked out by Es for interfering.
After waking up, Touya headed home. Hinata greeted him and told him that a guest had been waiting for over an hour to see him. Discovering that it was Es, he freaked out. He learned that Es had been assigned to guard him and tried to get answers about the situation, but only ended up more confused. Souichiro Unomaru and Mei Amanohokosaka then arrived and Touya was forcibly stripped by Es to search for a crystal. After taking a sample of his blood, Unomaru and Mei departed, leaving Es in the Himezuru residence.
When he woke up the next morning, Es was already gone. On the way to school, he recounted that he had slept on the couch because Es came into his bed while he was asleep to monitor him. After Es explained that she would follow any order, even if it meant dying, Touya got angry. Akira then arrived to join them and wanted to know what was going on with Touya. Touya begged Hinata to stay silent, but she ignored him and explained anyway, furthermore doing so in a way that caused Akira to misinterpret things. After Touya finally managed to explain himself, Akira told Touya to be more careful. Akira mentioned that there had been a gang fight in the Restricted Ward the night before, which Touya found strange.
At school, Touya was shocked to find that Es had transferred into his class to continue monitoring him.  After homeroom ended, Akira apprehended Touya and demanded to know what Touya's relationship with Es was. When Es said she was “to be in constant contact with Touya,” Akira misinterpreted her and became furious. Touya could only yell that it wasn't like that. Touya eventually managed to explain the situation to Akira. The relieved Akira then briefly hit on Es, but she was only confused by his introduction and desire to be friends, prompting Touya and Hinata to try to explain the concept of friendship to her. 
During a break, Unomaru arrived at Hakuo North Academy to talk to Touya. He told Touya that the Mitsurugi Agency had purchased Touya's school. They claimed it was a coincidence, but it was actually to facilitate transferring Es in so she could continue to guard Touya. He also explained that, for some reason, Touya could hear a Discover Call up to 300 meters away. Unomaru played on Touya's desire to protect people to try and convince him to use his powers to assist Es in tracking down Unions. When that failed, he played on Touya's guilt over surviving the Wadatsumi Incident, telling him that his mother, Ryouko Kagari, was responsible for both the incident and the resulting Union outbreak. After school, Touya told Es that he'd cooperate with the Mitsurugi Agency. Mei then arrived and, after hitting him several times, placed the Goofball Proximity Surveyor on his head.
After school, Touya saw Akira with someone he didn't know. He then heard a Discover Call from that direction so he and Es followed while Hinata went shopping. They found Akira and Kuon Glamred Stroheim after Akio Osafune fled, but Kuon quickly departed. After meeting back up with Hinata, he explained to them about Unions and that Es was guarding him but left out the connection between the Wadatsumi Incident and the Union outbreak. After getting home, he was greeted by Yuki Himezuru, who proceeded to tease him mercilessly before taking a bath. Once Yuki got out, Touya went to take a bath himself, but found Es and Hinata taking a bath together. Luckily, he managed to leave without being seen.
Having determined that Akio had most likely progressed to phase four, Es and Touya went out in order to find him.  Hearing Akio's Discover Call coming from the Restricted Ward, Touya and Es headed there. Once they arrived, they were attacked by Akio, with Es deflecting Akio's shots. Akio then asked Touya if he was “Touya Kagari” and demanded he hand over the Grimoire. Touya had no idea what he was talking about, so Akio decided he would kill him and take the Grimoire from his corpse. He prepared to launch a giant steel tower at Touya and Es, but Kuon destroyed it. She then introduced herself to Touya.
After Akio woke up, Es interrogated him, responding to his silence with violence, much to Touya's horror. Once Drei arrived, Es explained the Ten Sages and said that if Drei and Kuon were to fight, Kuon would lose. Es suggested they leave if that happened but Touya refused, saying he needed to help Kuon. However, he was interrupted by the arrival of Acht. Once Drei and Acht left, Touya's head started hurting. He saw Sechs and screamed until he passed out.
The next morning, Touya woke up in his room and ran out in a panic to find Es. He found her in the hallway and she explained that Kuon had also been assigned to protect him. Touya asked to speak to Kuon alone, so Hinata left with Es. Kuon then explained to him about Mages and told Touya that the reason the Ten Sages were targeting him probably had something to do with the Grimoire, but Touya claimed he didn't have it.
Touya then met with Akira and told him about Kuon staying with him. Touya got confused when Akira compared him to a video game protagonist and said he didn't see his situation as anything but a burden for Yuki. He then saw Mei and when he went to speak with her she told him that she'd protect him on her own so he shouldn't rely on someone from the Magic Guild. He was surprised to find that Kuon had also transferred into his class. 
Kuon called Touya and Es to the roof and told them about the Ten Sages and the Origin of the Grimoire. When asked why he was working with the Mitsurugi Agency, Touya explained that he was one of the Wadatsumi Incident's few survivors and had no memories before the event. He also shared with them the strange dream he'd been having, and that furthermore, since his mother had been in charge of the experiment that caused the Union outbreak, Touya felt it was his responsibility to help fix the problem. Kuon then promised to look into Ishana's database for information on the Grimoire.
Despite Es's suggestion to skip his part-time job due to potential danger, Touya insisted he had to go. Es agreed but said she would wait outside the entire time. They then saw police cars going by, but didn't do anything since Touya hadn't detected a Discover Call. At work, he had to put up with more of Ringo Akagi's antics.
After work, Touya and Es saw Mei in the area where they had seen police activity and went over to her. Touya got hit for sneaking up on her. While Mei worked, he asked Es what Mei was doing, causing Mei to yell at him for distracting her. Upon seeing Akio's dead body, Touya threw up. After finding the night watchman's body, Touya sensed a Union and warned Es and Mei. Es deflected a thrown knife, but Ripper threw a smoke bomb at them. Ripper appeared behind Touya, but Es drove him off. He and Mei followed after Es, but Touya was too slow so Mei decided to just carry him there while flying. After Ripper escaped, Avenge told Touya, Es, and Mei to leave Ripper to him and that he'd kill them if they got in his way. Touya approached him, saying he had no right to threaten people, but Avenge knocked him out for his trouble. He woke up to find Es carrying him home on her back, much to his embarrassment. Es apologized for allowing Touya to get hurt but Touya said it was his fault. Es asked him why he kept putting himself in danger and Touya explained that he couldn't stand seeing people get hurt and acted without thinking. He then requested that Es try to hold back from hurting people, but she said she couldn't promise that since it might interfere with her mission. Once they got home, they were greeted by Hinata, who took Es with her to the bath and told Touya to go in next. He then told Kuon about his encounter with Ripper. Kuon explained to Touya about Code: Embryo and that the Wadatsumi Incident and Grimoire were linked. 
Two days later he visited the pool with Hinata, Kuon, Mei, and Es, questioning Unomaru's intentions for bringing them there. They taught Es the meaning of fun in the process.
On the school roof during lunch, Touya told Es that he hadn't heard a Discover Call in a while and Es explained that it was because they had been finding many Unions who had been killed by Ripper. When Hinata joined them, he asked Es where her name came from but she didn't know. Kuon then joined and asked Touya if he was an anime fan, which he denied.
At the Himezuru residence, Es told him about the series of deaths caused by Gainart episodes. Kuon explained that it was caused by one of the Ten Sages and asked for his and Es's assistance in finding them and he agreed to help. At the location where Akio and his thugs attacked Akira, Kuon cast a spell on Touya that would let him detect magic so he could help find the wards placed around the city by the Ten Sages. Kuon told him about the Sealed Spear: Izayoi, Legacy Weapons, and the Sword of Destruction: Kusanagi, leading Es to look up information on them and tell him about the dangers of using Izayoi. Touya said he couldn't let her use it no matter what. Finding the last ward at the docks, the three encountered Sechs. He asked Sechs if he was a Union and the one turning others into Unions, which Sechs confirmed. When Sechs tried to use his Drive on Kuon, Touya got in the way. Touya yelled at Sechs for treating his sister like that, but Sechs merely found him interesting before leaving. After checking to make sure Kuon was all right, she asked for some time alone so he left with Es. 
Touya and Es arrived home to see Elise von Klagen staring at the Himezuru residence. Es told Touya about the ward around the house that should make it invisible to unauthorized people so anyone else who could see it was suspicious. Elise then introduced herself to them, explaining that she was sent by the Magic Guild and thanking him for taking care of Kuon. Elise tried to get him to admit that Kuon was being a burden but he said that it was his fault, not hers. Later Mei called Touya to learn what happened with Sechs, but she got mad when he said he was with Kuon, telling him how the Magic Guild ruined the Amanohokosaka clan. Kuon came to speak with him and Touya asked her about it, with Kuon concluding that it was probably true. She then asked Touya to go shopping with her and Elise since it would supposedly make Elise consider returning to Ishana. Touya was initially hesitant because it seemed pointless but Kuon convinces him it would be best if Elise left soon.
The next day, Touya was exhausted, realizing he was just brought along to carry their stuff. He and Es had a discussion about her thinking for herself, but Es simply said she couldn't ignore her orders. After they finished shopping. Touya asks Elise if she did this just to try and cheer Kuon up. Elise suggested going to a nearby café but Touya felt guilty having Elise buy something for him because it was attached to a five-star hotel. He was then approached by Hinata, who was out shopping with Akira. When Akira says he wanted Hinata to help him buy a gift for a girl, Kuon and Elise suggested they keep shopping. Toe was confused why they were splitting up so soon after meeting and had to be dragged away by Elise and Es. At the café, they spotted Acht. When Acht prepared to attack with Ice magic and Hinata came running in, Touya told Es to protect Hinata instead of him but she refused. Once Acht left, Hinata asked him if he was all right, which he confirmed. The next day on the school roof, he discussed with Es, Hinata and Kuon that Akira didn't show up for school. Once Hinata left, he was approached, and hit, by Mei, who demanded to know what happened the day before. Touya told her about the confrontation with Acht and Mei complained that she was getting more work, wondering why one of the Ten Sages was out in the open. Kuon and Mei got into a fight and he said they seemed to get along well, which angered the two and confused Es. Once Kuon left, Mei told Touya what she initially came to him for; that three more bodies had been found and someone who looked like Akira was spotted nearby, although Mei doubted he was responsible. Touya was adamant that Akira would never do something like that. After school, Kuon asked Touya and Hinata how long they've been friends with Akira and they told her about how their past. Akira would constantly get into fights and Touya would always charge in to break them up, getting injured in the process. They then split up to look for Akira while Hinata went home.
While searching for Akira that night, Es asked Touya why he cared so much about finding Akira. Touya said it was because he's a dear friend but Es didn't understand anything being important beyond completing her mission. She found it strange that Touya was being allowed to roam free so Touya suggested she ask Unomaru but she said she had been unable to reach the Mitsurugi Agency. Touya then heard a Discover Call coming from the Himezuru residence and they ran off in a hurry.  They arrived home to find Acht holding an unconscious Hinata. Es told Touya that Acht was too powerful for her to defeat so they should give up on Hinata and escape, something that made Touya furious. He ran in to save Hinata himself, but Acht simply blasted him away with Ice magic. Acht prepared to finish him off so Es ran in to attack, prepared to kill Hinata to save him. As Touya screamed for Es to stop she was restrained by Akira's Drive. Akira then knocked her out and attacked Touya, knocking him unconscious. Once Touya woke, up Kuon told him what happened and that he should stay in the house while she and Elise searched for Akira, which Touya agreed to. Touya ran into Es and demanded to know if she was seriously planning to hurt Hinata. When Es didn't answer he walked away, saying he couldn't stand looking at her right now. Touya became angry that everyone was searching for Akira while he was sitting there doing nothing. Yuki then appeared behind Touya, surprising him. Over coffee, he confided in her that he put Hinata in danger and was being a burden to her but she denied this, saying Hinata would be fine.
The next morning, Hinata woke up fine, having been asleep through the entire event. She told Touya that Es was worried about him and stayed outside his room the entire night but he quickly left. After Kuon and Elise leave, Es told Touya that she would take a three-hour break and that she informed Mei about this. He wondered if something was wrong since Es had never taken a break but then recalled Es trying to abandon Hinata. Touya took the opportunity to sneak out and search for Akira before Mei arrived. Before he could get away he got caught by Mei, who decided she would accompany him somewhere close by. He chose to go to Maha Raja. After meeting with Ringo, and being teased for bringing another girl, Mei told him about the history of her clan. Es then arrived and took him back home. Once they got home, Kuon said she needed to talk to Touya and Es, telling them about Akira's unnatural crystal progression and that they needed to stop him before he reached phase five and was marked for termination. She said that nobody had survived being Union-infected and Touya should prepare for the worst. Touya went back to his room and was greeted by Hinata, who asked to spend some time with him since she was worried about Akira. Touya fell asleep and found Hinata had left when he woke up before remembering about Akira. He then received a phone call from Akira, who told him to come to the school alone. In order to get past Es, he told her he heard a Discover Call coming from the abandoned factory. When Es pointed out that it was more than 500 meters away, outside the range of Touya's ability, he told her it was an order, so she went.
Touya found Akira on the roof and told him to come with him, but Akira said he was too far-gone and attacked Touya, seeing Touya as nothing but an enemy. Before Akira could kill Touya, he was saved by Es. Es said she followed him despite being required to follow orders and wasn't sure why she did this. Es was unable to stand up to Akira's attacks and asked Touya to run away while she distracted Akira, even saying “please.” Touya angrily asked if she was planning on having him abandon her as well but she said it was okay since she wasn't part of his family. When Es and Akira went to attack each other, Touya jumped in the way of their attacks, saying he didn't want them to kill each other. Touya reminded Akira that he used to jump into Akira's fights like he just did and that Akira promised he wouldn't fight anymore, bringing Akira back to his senses. Akira then ripped the crystal out of his arm. After collapsing, Akira apologized for breaking his promise before falling unconscious.  After Akira was taken to Shin Yokozaki University Hospital, Unomaru finally contacted Es and told her to return to the Agency so she said goodbye to Touya. However, right before she left, she told him to wait by grabbing his sleeve. Es apologized to him for what she nearly did to Hinata. Touya apologized as well and Es asked if he liked her again. Touya freaked out until Es explained that Yuki told her to make up with him. Touya said he wanted to make up with her as well and Es became very happy. Es then left. 
The next day at the hospital, Touya learned that Yuki was aware of the Union outbreak and she told him about Akira's condition. That evening, he told Kuon that Es was able to return to the Mitsurugi Agency and Kuon breaks her promise to Mei, telling Touya about Es being an artificial human. They were then approached by Unomaru. Once Kuon left Touya asked Unomaru about Es and, despite claiming it was confidential, he told Touya that she was a Prime Field Interference Manifestation. Touya didn't care about that, wanting to know why Unomaru abandoned Es. Unomaru claimed that it's because he was close to finishing developing the new version of Es and when he became focused on something he couldn't pay attention to anything else. Touya was horrified by Unomaru's callousness towards Es, with him calling her a thing and assuming Touya was worrying more about what happens to her body once she died then about keeping her alive. When Unomaru was about to leave, Sechs, Drei and Acht suddenly appeared behind them. Touya demanded to know why Sechs turned Akira into a Union but Drei said it was because Akira wished for it. Sechs asked Touya what he desired from the world but Touya didn't answer, merely wanting to know why Sechs turned Akira into a Union. Sechs said it was to show Touya the truth and asked him what he wants again. Touya said he wanted to protect people from being hurt by people like Sechs, but Sechs asked him what he'd do if his existence caused people harm. He told Touya ask himself why he exists before he, Drei and Acht disappeared. Unomaru called them rude for just showing up, lecturing people and leaving and said he had no idea what they're trying to accomplish before Touya heard a Discover Call coming from Akira's room and ran off.
Touya reached Akira's room but only found Kuon there; who told him that Hinata went shopping. He then received a call from Hinata's phone, but it was actually Ripper, who had kidnapped Hinata. Touya asked if this had something to do with the Grimoire, but Ripper said he forgot he was asked about that, only doing this because he found Touya interesting. Ripper told Touya he had to find them before sundown or he'd kill Hinata and hung up. On the way out, Touya saw Yuki, who saw Kuon run out of the room and Yuki asked if she was going back to the house. Touya lied and said yes before telling her he had to go. He frantically ran around the city but had no luck finding her. After running into Kuon, he received another call from Ripper, who said he was tired of waiting and activated his Drive so Touya could follow the Discover Call to him. With the help of Kuon's magic, they reached Ripper and found Hinata unconscious and hanging over the edge of the roof by a chain. Touya begged Ripper to let Hinata go, but Ripper just made fun of him. Ripper told Touya that he had a strange “odor” similar to his own and Sechs's and he wanted to find out why that was for fun. In order to make Touya unleash his power, Ripper told him that he was the one who murdered Yuki's parents. When that didn't work, Ripper cut the chain holding Hinata, leaving her to fall to her death. Touya went berserk, unleashing the power of the Origin of the Grimoire, which stole the seithr from Ripper's body, causing him to run off saying it's not fun anymore. Unable to control himself, Touya also sapped Kuon of her strength. Mei arrived, healing Kuon, alongside Es, who revealed she caught Hinata and she was fine. This caused Touya to return to normal.  Once Touya woke up, Mei promised to tell him and Kuon everything she knew but suggested they return to the Himezuru residence since it was too dangerous where they were.
Back at the Himezuru residence, Es told Touya that Hinata was all right and Touya thanked her. Mei called for Touya to come down so he asked Es to keep an eye on Hinata for him, which she agreed to. Touya thought that Es seemed different but was pulled out of his thoughts by Mei yelling at him. Mei told him about Unomaru's plan and about the Gate of Sheol underneath the Wadatsumi Research Facility. Mei then told him and Kuon about the Amanohokosaka's history guarding the Gate and that the first Azure Shrine Maiden stopped the Black Beast from emerging by luring it back into the Gate and sealing both of them inside it. Touya had doubts that Unomaru was planning what the Ten Sages said he was, which angered Kuon. This led to Kuon and Mei getting into a fight, which Touya hopelessly tried to stop. Kuon then left, saying she was going to speak to Sechs one more time and that she'd probably never return to the Himezuru residence. Mei told Touya that she would be guarding Touya from then on in case the Grimoire went berserk again, but he was worried about Kuon and ran off. Touya was unable to find Kuon and wondered if she should have left it to Es and Mei. Es found him, telling him that he had been classified as a high-risk Union by Unomaru and she had been ordered to bring him in. Learning that Mei was in charge of the unit searching for him, Touya said he needed to find Kuon and asked Es to wait on capturing him until then, but Es said she wanted to guard him. Touya refused when she said she'd be killed for disobeying orders and he said she'd be at risk if he lost control again, saying she was too important to lose. Es promised that if Touya ever lost control of the Grimoire she would stop him no matter what so that he could not hurt his loved ones, which he agreed to. Before they could escape into the sewers, Mei found them. Touya told her about Es's promise to kill him and Es said she knew she would die for betraying the Mitsurugi Agency, which caused Mei to yell that she quits in frustration, saying the two needed to care about their own lives more and consider how those close to them would feel if they died. Mei told Touya she would find Kuon so he should focus on escaping. Mei covered for them with a smoke bomb and they escaped underground. They were nearly caught by agents from the Mitsurugi Agency but were rescued by Avenge, who took them to somewhere where they'd be safe. Touya wanted to know why Avenge was helping them and Avenge said it was because he felt like it. Touya thanked him, but Avenge said he should be thanking Touya for allowing him to kill Ripper. Touya didn't know how to feel about Ripper being dead and Avenge said he was stronger then he seemed. Avenge said that he was basically a serial killer who was no different than Ripper for hunting down and killing Unions, but he could live with it as long as he was aware of it. He then told Touya that, while he didn't kill Ripper himself, it was his actions that led to Ripper's death and he must accept that, with Touya saying yes. Avenge then asked Touya if he wanted to know about his mother's role in the Wadatsumi Incident, even if he'd be better off knowing. Touya grabbed Avenge and demanded to know. Avenge told Touya that the Takamagahara Group was forcing Touya's mother to build the T-System and that the Embryo was meant to be its core. Touya was shocked that it meant Unomaru was doing as the Ten Sages said, which surprised Avenge that Unomaru was continuing Takamagahara's research. Es then explained about the Embryo's power to use Phenomenon Intervention and that with it, it would be possible for the T-System to control the thoughts of everyone on the planet. Es said that the T-System would be impossible since they didn't have an energy source big enough for it but Touya realized that they intended to use the Boundary and its infinite supply of seithr. Suddenly Es detected a large number of Mitsurugi Agency soldiers and Avenge told them to go ahead while he dealt with them.
After they left and discuss what to do next, they were attacked by Drei. Drei claimed he was aiming for Es, calling her a “doll.” Touya angrily claimed that Es was no different from a normal human but Drei said that artificial beings are not part of Sechs's plan and therefore cannot exist.  Drei attacked Es but Touya took the attack for himself. Drei told Touya to stand aside and watch him kill Es, attacking her again. As Touya started to lose control, he told Es to fulfil their promise but Drei stopped Es from killing him. Touya screamed for Drei to stop attacking Es and suddenly found himself surrounded in pitch black where a mysterious man, taking the form of Ripper, told him he's inside the Grimoire. Ripper explained that Ripper was dead but he is an illusion created by Touya. He then attacked Touya. A version of Es appeared behind Ripper and Touya was forced to watch as she was cut apart as well. Ripper said that it was Touya's fault Es was dead because if Touya had killed him this wouldn't have happened. Ripper then stabbed Touya repeatedly, telling Touya he was weak for not wanting to kill people. When Touya said he didn't want to die or kill people, Ripper suggested that means it's okay to hurt people, which Touya was unable to answer. Ripper then said he'd let Touya use the Grimoire a bit, activating “Code: Soul Eater, Limited Penance” and saying they'll speak again. Back in the real world, Touya unleashed the power of the Origin of the Grimoire on Drei and told Es to get behind him. Es asked if he could control the Grimoire and Touya said he didn't know but it felt like he could. When Touya refused to back down, Drei said that he could still break every bone in Touya's body, as long as he didn't kill him. Touya threatened to unleash the Grimoire again but nothing happened. As Drei was about to attack, he was stopped by Avenge. Avenge told Touya and Es to leave Drei to him and run to Mei. Touya thanked Avenge and he and Es ran off.
After they escaped, Touya asked Es if Avenge would be all right and Es said it was possible since Drei was weakened. Es then asked Touya if he could control the Grimoire, but Touya said he wasn't sure he had a hundred percent control since he couldn't use it then. Es collapsed but Touya caught her. Touya apologized, saying she was probably cold because Touya's clothes were wet but Es said he was very warm. Emerging from the sewers, the two encountered Mei, who said she still hadn't found Kuon. Mei yelled at them for smelling and said she had a spare set of clothes for Es. Mei told Touya to go home and get a change of clothes and when Touya asked if he would be safe there, she told him that Elise had sent out a false lead that Touya was on a bullet train away from Shin Yokozaki City. Touya wanted to tell Mei about the T-System and the Ten Sages, but Mei revealed she had Avenge put a wiretap on him and already knew about it. They decided to head back to the Himezuru residence and were greeted by Hinata. Hinata grabbed him and told him to go and get changed. After getting changed, he found Mei, who told him about Kuon while insulting her. Kuon told Touya and Mei to meet her downstairs since she had important information from Elise. After Hinata left, Kuon read a letter from Elise that contained her findings about the Wadatsumi Incident. She discovered that Unomaru was a survivor of the incident and that he was not working to treat the Unions he captured, but rather to gather their crystals so he could refine the Embryo. She also found that TOi is powered by the T-System and was created to be a high-level information control system. They figured out that Unomaru was likely at the Wadatsumi Research Facility attempting to complete the T-System. Mei said Touya should stay behind because of the Grimoire and because it was too dangerous, but Touya said he had something he needs to ask Unomaru. Kuon said they should bring Touya along and promised to kill him if he lost control so Mei agreed but said she'd send him home if things got too dangerous. They then discussed that they needed to deal with the Ten Sages, Mei revealing that Avenge told her that he had killed Drei. Mei theorized that the Origin of the Grimoire was the only thing that could destroy the Embryo and the Ten Sages had been trying to cause Touya to activate it for that reason. Mei asked if they had anything they needed to do before they head out and Es asked for pudding so Mei begrudgingly said they'd wait until Hinata returns. Touya then received a call from Yuki. Yuki said she couldn't come home that night but she had some good news before giving the phone to Akira. Akira apologized for making Touya worry. Akira asked Touya if he was about to do something stupid but said Touya would be fine. After taking the phone back, Yuki told Touya that Akira was fine but his rehabilitation was going to be hell. Touya said they need to have dinner together again soon and Yuki said of course they would since they're family and hung up. Touya then told Kuon and Mei that Akira was going to be all right. Kuon was relieved but Mei said she found his ability to survive gross like an insect. Just as Mei complained about Hinata taking a long time to get back, she arrived with pudding. Touya then told Hinata that they would be out late and she shouldn't wait up for them but she insisted she would. 
Arriving at the Restricted Ward, Mei found it odd that there was no one there. Es didn't detect any human presence inside and said if they were going to go inside they should do it now. Inside, Touya recalled how he first met Es. This caused Kuon and Mei to get in another fight, with Mei saying she couldn't believe she was working alongside someone from the Magic Guild. Kuon promised that she would force the Magic Guild to change its ways once she got back to Ishana but Mei must reclaim Wadatsumi in exchange. Mei accepted and they approached the wall around the Wadatsumi Research Facility. They were suddenly attacked by Acht's Ice magic. Es deflected all of the attacks and Acht remarked that she hoped to kill at least one of them with that attack. Acht said she had no idea where Sechs was and was no longer involved with him; she just wanted to go crazy. Acht said that they must defeat her in order to go on. She told Touya to go away since she didn't want to deal with him, but then said she was just kidding and attempted to kill him. However, Es protected him. Acht called Touya pathetic for always having others protect him. She then attacked him again but was intercepted by Mei, who told Touya to go home and he ran off.
Touya called himself pathetic for not being able to fight. He wondered why he was able to control the Grimoire against Drei and tried to use it again but nothing happened. Touya decided to try and talk to Unomaru and convince him to stop refining the Embryo as well as ask him about his mother and why he was at Wadatsumi during the incident. Upon reaching the Wadatsumi Research Facility, he was met by Es, who asked why he hadn't returned home. Touya asked Es why she was there and she said she figured Touya wouldn't listen to Mei based on his past actions. Touya said he meant what would happen to Kuon and Mei without her but Es said she had confidence that they would be okay. Touya said he didn't want anything to happen to her, but Es countered that she made a promise to him and Touya apologized for trying to break it. They then headed in together.
Inside the Wadatsumi Research Facility, Touya and Es found it odd that they hadn't run into anyone yet. Es said that they had passed many security systems and none of them had activated, suggesting this was a trap. Suddenly, they were confronted by an Es-N unit and Unomaru talked to them over the speaker system. Unomaru told Touya to go into an elevator and come down to him if he wanted to talk, but specified that only Touya was welcome. Unomaru called Es garbage and ranted about how much superior the Es-N were, which angered Touya. Unomaru told the Es-N to kill Es and capture Touya so Touya and Es ran. Es said that she would stay and fight Es-N while Touya went on ahead. Es told Touya that she had killed many Unions without questioning orders but she had realized that what she did was wrong, saying she had committed so many sins she was beyond redemption, but hoped to try by protecting Touya. Touya went to confront Unomaru while Es stayed to fight Es-N.
Touya took the elevator down to the core of the T-System where he was greeted by Unomaru and four more Es-N units. Unomaru revealed that he had created eight of them, with another on the way and had sent reinforcements to take care of Es. Touya said he needed to go back, but Unomaru told him he had locked the door behind Touya. Unomaru thanked Touya for coming to him and making things easy, but Touya said he came to stop Unomaru from refining the Embryo. Unomaru asked him why he'd want to do that, saying that humanity would destroy itself within a century if left on its own. Unomaru told Touya the story about his parents and said he wanted to end pointless fights and help humanity reach its full potential. Touya said he might have had a point but it was wrong to manipulate people like that and he was afraid people would stop thinking for themselves. Unomaru then told Touya that his mother was also opposed to the T-System and during the Wadatsumi Incident she shut down the T-System right before it was completed, causing the incident, but she managed to contain the damage to just the Restricted Ward. Angry that she stopped the T-System, Unomaru doctored documents to make it seem like Ryouko Kagari was in charge of the experiment and blamed the incident on her as revenge. Touya called Unomaru insane since his mother was just trying to save people but Unomaru said Touya was the same since his Origin of the Grimoire was what caused the Black Typhoon that engulfed the Restricted Ward. Unomaru said it's time to refine the Embryo, which confused Touya since he came to stop it, but Unomaru countered that refining it would have been impossible without Touya. He then ordered the Es-N units to release the Grimoire and they pinned Touya to the ground with their swords. Unomaru told Touya that the Es-N's weapons were made from Mei's blood and had the power to control the flow of seithr, allowing them to forcibly control the Origin of the Grimoire.  Unomaru then revealed to Touya that Hinata was Code: Embryo, causing Touya to become enraged and start unleashing the Grimoire, which Unomaru said just saved him work. Unomaru had Touya absorb the seithr of all the Unions' crystals he'd collected and give it to the Embryo, completing the Embryo and opening the Gate of Sheol to the Boundary. Unomaru said all he needed to do was go to the T-System's control room and activate it in order to take control of the world. He also said he needed to hurry since leaving the Gate open for too long could kill everyone. Unomaru started going mad with power, saying he felt like he could do anything and laughing maniacally. However, Sechs suddenly appeared and stabbed Unomaru with the Sword of Destruction: Kusanagi. Sechs said that Unomaru's time had come. Unomaru ordered the Es-N units to kill Sechs but Sechs effortlessly defeated all of them. As Sechs turned his attention to the Embryo, Unomaru started stumbling forward, saying he wouldn't lose to Sechs but fell into the Boundary.
Es arrived at the core of the T-System to find Sechs in front of Hinata. Es ran over to Touya, asking him if he was all right and what'd happened. Touya told Es that Hinata was the Embryo, that Sechs was going to kill her and that he had already killed Unomaru, asking Es to save Hinata. Es told Sechs to get away from Hinata but Sechs called her a “doll” and told her if she got in his way he'd eliminate her as well, attacking her with the Sword Of Destruction: Kusanagi. Es wondered how any human could have that much power and Sechs explained that it was because of the Kusanagi and Hinata's Phenomenon Interventions. Sechs said that destroying the Embryo would free the Boundary, flooding the world with seithr and melding everyone's souls into one. Sechs then fired the Kusanagi at Hinata, who fell into the Boundary. Touya tried to jump into the Boundary after Hinata, but Sechs said he would send Touya back to seithr and attacked him with Kusanagi, knocking him unconscious. Once again, Touya met with “Ripper” in a black void. Touya told Ripper to send him back so he could save Hinata, but Ripper said this wasn't the time for that. Ripper encouraged Touya to get angry, saying he'd be swallowed if he stayed weak, Touya said he didn't care, he just needed to get out of there and Ripper told him he could leave as long as he accepted “it.” Ripper then goes on that the strong eating the weak was the rule of the world and that Touya had already started to accept it when he gave in to Ripper's earlier suggestion that it was okay to hurt people. Touya asked if Ripper was asking him to kill, with Ripper replying that Touya could either die or accept the burden of living. Touya said he'd made up his mind; that he wanted to protect those dear to him, even if it meant committing sins. Touya was then transported to a white void where he met with another version of himself. This Phantom Boy asked him to say their name. The Phantom Boy said that “Touya Kagari” was the name that the Grimoire came from and revealed himself as the arbiter of the Origin of the Grimoire. Touya was confused, since he was supposed to be “Touya Kagari” but the Phantom Boy said that the two were one and the same. The Phantom Boy also said that in order to use the Origin of the Grimoire, one needed a strong spirit and if one tried to force its use they would lose themselves; revealing that he had been born when Touya lost control. The Phantom Boy said he didn't know if it happened because they had absorbed Ripper's seithr or for self-preservation but the reason didn't matter. He continued on that he would teach Touya special words that would let him channel the power of the Grimoire through his body. Touya woke up back in the real world and saw Kuon and Mei unconscious, wondering where Es went before Sechs told him she had returned to the seithr. Touya demanded to know why Sechs could kill people so easily and to bring everyone back but Sechs said not to worry since Touya would soon be returned to the seithr as well. As Sechs prepared to strike, Touya heard Es's voice telling him not to give up and to say those words. Touya then picked up the Signati Gladio Crystalis: Murakumo and said “Code: Soul Eater. XBLAZE, ignite!” Activating the true power of the Origin of the Grimoire, Touya declared that he would stop Sechs and attacked him. Touya was able to hold his own against Sechs's attacks for a while but Sechs said Touya would not be able to scratch him with that level of power and began his attack anew, overwhelming Touya. Sechs told Touya that he had grown stronger each time the world had been remade and even with the Origin of the Grimoire, Touya alone could not win. Touya then heard Es's voice telling him to come to her.
Using the Embryo's powers, Es pulled Touya into an enclosed space with her. Touya asked what happened to Hinata and Es reassured him that she had restored Hinata's body and returned her to the Himezuru residence as well as that when Hinata woke up she would not remember that she was the Embryo. Es said that with Phenomenon Intervention she could return everything to when it was peaceful, but it would not work against Sechs because he had the Kusanagi. The Sword of Destruction: Kusanagi nullifies Phenomenon Intervention and so Sechs retained his memories whenever the world was reset. Es told Touya that Hinata had already recreated the world many times without control of the Embryo. Hinata had done this to try and protect everyone but each time distortions would occur and Sechs would get stronger. Touya asked Es if there was anything he could do and Es responded that only he could do something about it. Since this phenomenon was born from an event in Touya's past, the current version of him should have be able to change it. Es told Touya that she would send him to where everything began, the first iteration of the world and once he got there he must eliminate a Union. Es apologized that she was forcing Touya to kill someone but it was the only way. Touya understand that this was a sin he had to endure and accepted. Es told him he only had one chance to intervene and sent him to the past. Touya heard a Discover Call and followed it to Sechs in the Restricted Ward. Touya and Sechs charged at each other and Touya managed to shatter Sechs's crystal. This destroyed the crystal of the Sechs in the present as well and he fell into the Boundary.
Back in the enclosed space with Es, Touya said he could still feel the sensation of cutting Sechs's crystal and realized this was what Es had been feeling all this time. Es welcomed Touya back and told him that Sechs had returned to the Boundary and the distortions of the past had been erased, allowing the future to continue on. Es said that Touya was able to protect everything like she knew he would. Touya told Es they should return home but Es revealed she could not return. The Embryo was a threat to the world and it would create more distortions simply by being in the real world. Es said that this was goodbye, but Touya yelled for her to wait and that he couldn't leave her now. Touya says he hoped that they could stay together forever. Es then kissed him and said everything would be all right. When he returned he will have forgotten about Es. Touya screamed Es's name as she said goodbye to the person most dear to her.
One month after the Embryo incident, Touya, Kuon and Mei were chasing a Union and Touya could tell they were in phase four just based on their Discover Call. They found him and noticed he was acting unnatural and his clothes were damaged. Not wanting to prolong the fight since they were not in the Restricted Ward, Touya activated XBlaze. Touya asked Mei if she could use a spell to restrict the Union's movement since he didn't want to hurt him. Together the three managed to subdue the Union. Mei said she's glad she had Touya and Kuon's help and Kuon realized that it meant Mei was understaffed. Mei then told them that she was reprogramming the last Es-N unit to work for them but she was having trouble switching its power sources from crystals to electricity. Mei said that the unit would probably be less efficient like that, but was sure she can compensate with her magic. Kuon made fun of Mei's style for thinking a robot familiar was cool and the two got into an argument. Touya tried to break it up but the two insisted they were having a normal conversation.
Touya had another dream where he was in a white void and met with the Phantom Boy. Touya thanked the Phantom Boy for giving him the power to defeat Sechs. The Phantom Boy told Touya that they'd already had this conversation more than twenty times but whatever happened in this place was just a dream to Touya. The Phantom Boy then said Touya that needed to leave this space immediately and he was fine with letting the unknown remain unknown. He said Touya needed to forget about him, since Touya needed to start being himself without the Phantom Boy's influence. Touya said he didn't want to forget, no matter how sad the memory was. The conversation then turned to Touya's mother and Unomaru, with Touya saying he wanted to learn the truth about everything and he would be able to accept it. Touya then started to fall asleep and the Phantom Boy said the truth might be more than Touya could handle.
The next day, after researching the Wadatsumi Incident again, Touya came downstairs to find Kuon and Mei. Mei said she came to say goodbye since Kuon was returning to Ishana the next day. Kuon said that Mei shouldn't have come if she was busy but Mei said it was important, which Kuon found endearing. Touya said he wanted to talk to them in private. Touya said it was about his lack of memories from before the Wadatsumi Incident and why he was at the Wadatsumi Research Facility in the first place. Mei realized that it was suspicious that Unomaru had so much information on Touya from the very beginning. Touya begged the two of them to help him find out more about his past, which the two readily agreed to. Mei said she owed Touya a favor for helping her with her work, since his promise to help the Mitsurugi Agency ended with Unomaru's death. Kuon said she'd have Elise look into Touya's past, since she's good at uncovering information. Mei said she could get in touch with Avenge to ask him about it since he was one of the few people who knew about the Takamagahara Group. As Touya thanked them, Kuon and Mei said Touya had changed since they first met since he no longer just said “sorry” to everything. Hinata arrived, agreeing with them. Touya asked if she heard the whole conversation but Hinata said she was making tea. Later, after Yuki arrived, Kuon said she needed to leave. Kuon thanked Touya for everything, saying that even if she lost her brother, she would treasure the days she spent with him and the others. Yuki started teasing Touya about Kuon but was disappointed to find out Touya just asked Kuon to do him a favor. Kuon then left. 
10 days later, Ringo was at the Himezuru residence and tried Hinata's curry, praising her skill. Touya and Mei found it strange that Hinata was able to have a normal conversation with Ringo. Mei said the curry looked good but Touya was sick of it, wondering how long Ringo planned to stay at their house. Mei updated Touya on the progress of his request; that she had a found a journal kept by Unomaru but she hadn't been able to open it yet. She also told him that the Mitsurugi Agency operated internationally and that the scope of it was far beyond what they expected. Touya then received a phone call from Kuon, but it turned out to be Elise. Kuon took the phone from Elise, saying she was embarrassing. Ringo interrupted, saying she would leave now that she'd stolen Hinata's recipe, which relieved Touya. Ringo said she didn't expect to see Touya any time soon and left. Kuon was surprised to find Zwei at the Himezuru residence but Touya had no idea what she was talking about. Kuon also gave Touya an update; saying she found out how the Origin of the Grimoire ended up in Wadatsumi. 10 years ago, the Magic Guild and Takamagahara cooperated to open the gate to the Boundary. Takamagahara wanted the infinite energy source of seithr while the Magic Guild wanted to find the “Roots of the Azure.” The Magic Guild had members of the Ten Sages try to force open the gate and they were lost in the Wadatsumi Incident. Elise told Kuon they needed to get back to their room since the dorm manager was making her rounds so Kuon hung up in a hurry. Mei said that, while they had learned some new information, if they wanted to get to the truth they needed to open Unomaru's journal. Touya asked to visit Unomaru's office, even if it was pointless. Mei agreed, saying he might find something with his main character-like personality. Mei then gave Touya the key card to Unomaru's office. Hinata called that the curry was ready, but Touya was sick of it after having eaten it for 10 days.
Touya visited Unomaru's office and was surprised to find Unomaru's collection of frilly dresses. Suddenly Touya had a flash of memory from the Wadatsumi Incident, watching Unomaru. In the Restricted Ward, Touya recalled all of the events that had happened there. When he tried to remember who saved him from Goro he found himself unable to remember them. He was then approached by Avenge, who said Mei told him to come. Touya explained to Avenge about his desire to regain his memories and wanted to ask Avenge what kind of person his mother was. Avenge said he didn't care whether or not Touya got his memory back and started to walk away. Touya begged him to say anything since he was the only person who knew his mother. Avenge claimed he had only talked to her a couple of times. Avenge told Touya that his mother worked as a scientist at the Wadatsumi Research Facility and that he had been hired by the Magic Guild as a bodyguard for a high-ranking mage. Avenge said he never spoke to Touya's mother, but did once run into her when she was speaking to Sui Amanohokosaka, Mei's mother. Ryouko was talking about how she had to protect something and would do whatever it took to do so. Avenge then told Touya that even though he was found in the Restricted Ward after the incident, he had not seen Touya in the days leading up to the incident. Avenge prepared to leave again, saying that he told Touya he wouldn't be able to help him regain his memories, but if he couldn't let go, he needed to keep fighting. Avenge then left.
Another day, Mei called Touya back to Unomaru's office, saying she managed to decipher quite a bit of Unomaru's journal. First, Mei explained that, despite everyone who survived the Wadatsumi Incident losing their memories, Unomaru regained his quickly thanks to his journal. Mei said that despite how difficult Unomaru's cipher was, she managed to learn about most of Touya's past. Touya thanked her but Mei said she hadn't said she would tell him anything. Mei told Touya to promise he'd always be Touya Kagari, no matter what he learned. Touya promised to do so. Mei explained how the original Touya died and the current Touya was the Origin of the Grimoire transformed into a clone of him. Touya freaked out, blaming himself for the Black Typhoon of the Origin of the Grimoire that killed 3000 people. Mei said that it was likely that the transformation actually stopped the Black Typhoon from killing everyone in Shin Yokozaki City but Touya was skeptical since it was merely speculation. Touya said that Mei didn't seem surprised about him not being human, but Mei responded she was surprised when she learned about it. However, it would not change how she felt about him. Mei then prepared to go home, reminding Touya not to forget his promise. 
At the Himezuru residence, Touya wondered what he was. Hinata came into his room, asking if he wanted to come with her to visit Akira. Touya agrees and they went to the hospital. After greeting Akira, Touya apologized for not visiting him more often but Akira said it was fine since he was busy helping Mei. Akira told Touya that he finally had found a goal to strive for; he wanted to be a doctor. Having been stuck in the hospital, Akira started looking up to Yuki after seeing her work and decided he wanted to be like her. Akira said it was silly but Touya found it amazing. Akira countered that Touya was the amazing one since he was doing something no one else could. Akira asked if Touya remembered when he went crazy and Akira revealed that he did remember. Akira remembered that Touya jumped into harm's way to protect him and he thanks Touya since he probably would have died had Touya not done that. Hinata came in, apologizing for being late since she had been talking to Yuki. Hinata accidentally revealed that she told Akira to try and cheer Touya up since he seemed depressed and that was the reason for the visit. Hinata and Akira told Touya he could talk to them about anything but Touya said it was something he had to solve on his own. He then received a phone call from Mei, so he said goodbye to the two.
Outside the Restricted Ward, Touya talked to himself, saying he felt a little better after speaking to Akira and he would definitely find the answers he was looking for. He then met Mei in Unomaru's office. Mei noticed that Touya seemed much happier and Touya said it was thanks to Akira, which surprised Mei. After a brief argument, Mei tried to get down to business, telling Touya she had found out more information about how the original Touya died. She said that this information wasn't from Unomaru's journal, but from Ryouko Kagari's notes. She explained about Hinata, the Embryo, being brought to the Wadatsumi Research Facility 12 years ago and the experiments that were performed on her, as well as the circumstances of Touya's death. This led to Touya and Mei's mothers turning against the Takamagahara Group. Touya tried to thank Mei but Mei said it was fine since she got to learn more about her mother and thanked Touya. They lightly chatted about fate bringing them together as a team like their mothers were. As Mei was about to leave, Touya stopped her, telling her he wanted to officially join Sleipnir and Mei accepted. Mei told Touya to start treating her with more respect since she was now his boss but found it too weird. She then gave him a flash drive and told him to look at it when he got home. Mei then asked Touya if he had someplace he had to be and he said yes, so she told him to get going.
Touya went to visit Akira again and was surprised to find Hinata was there. Hinata excitedly told him that Akira would begin his rehabilitation the next day. Akira noticed that Touya looked contented and Touya said he settled a lot of things. Hinata got jealous of their friendship between “bros.” Touya wanted to tell them about his decision, but he suddenly heard a Discover Call coming from the school. Touya left, saying he would see them tomorrow. On his way out he ran into Yuki. Yuki asked why he was in a rush and when he said it was for something only he could do, she told him to get going so he ran off.
Back at the Himezuru residence, Touya used the flash drive Mei gave him and found a video of himself when he was young and met Hinata for the first time. 
One month later, Touya woke up after school to Hinata's humming. Mei arrived and apologized for being late. Touya said he needed to get going and Hinata wished him luck with his new job, saying it was a shame Maha Raja closed so suddenly. Touya tried to say that it wasn't a job but decided it was close enough. Hinata then told Mei that she had received mail from Kuon, saying that she had made it back to Ishana safely and to tell Mei that she would keep her promise on the honor of the true Ten Sages. It also said that, due to Elise's insistence, they would be back in Japan soon. Mei said that meant they'd just have to work even harder. Mei then told Touya to move out and not to fall behind. In the Restricted Ward, Touya recalled that thanks to Mei and Elise the Embryo incident was mostly covered up. Additionally, Mei intended to build the Amanohokosaka clan's headquarters there, not wanting to be reliant on the Mitsurugi Agency forever. Touya had been using his abilities to help Mei track down Unions. Touya asked about the Union they were supposed to be chasing but Mei said that Es-N had already taken care of it so Touya said he'd see her at school.
The next morning, Touya and Hinata greeted Yuki in the hospital and Hinata asked about Akira's condition. Yuki said he'd started walking and was slowly getting better and it was okay for them to visit him. Yuki told them that since he was scheduled for rehab, he was probably in the garden. After finding Akira, Touya said he looked like he was doing great but Akira said he could barely move his hands and felt useless. Hinata said she brought Akira some pudding, saying that pudding was happiness. Akira asked if Hinata was going to feed him and she said of course. Akira said it was a bit embarrassing, but Hinata had no idea why. Touya then had flashes of memories about Es and started crying but he didn't know why. Touya ran off to wash his face. Touya then thought to himself that his feelings for a special someone had suddenly burst out but he could not remember anything. However, Touya was sure that he was connected to that person and that someday he would be able to meet them again. 
- BlazBlue 10th Anniversary Site, Touya Kagari
- XBlaze Code: Embryo, Episode 1
- XBlaze Lost: Memories, Azure Main Memory 02
- XBlaze Code: Embryo, Episode 2
- XBlaze Code: Embryo, Episode 3
- XBlaze Code: Embryo, Episode 4
- XBlaze Code: Embryo, Episode 5
- XBlaze Code: Embryo, Es & Hinata Route Episode 6
- XBlaze Code: Embryo, Es & Hinata Route Episode 7
- XBlaze Lost: Memories, Azure Main Memory 04
- XBlaze Code: Embryo, Es & Hinata Route Episode 8
- XBlaze Code: Embryo, Es & Hinata Route Episode 9
- XBlaze Code: Embryo, Es Route Episode 10
- XBlaze Code: Embryo, Es Route Episode 11
- XBlaze Lost: Memories, Black Stone Sub Memory 01
- XBlaze Lost: Memories, Black Stone Sub Memory 02
- XBlaze Lost: Memories, Black Stone Sub Memory 03
- XBlaze Code: Embryo, Es Route Episode 12