Born to a large and poor family in the 11th Hierarchical City of Shinatsu, Makoto has faced countless amounts of prejudice in her life because of her species, making her detest most humans for their behaviour. She entered the Military Academy so her family could have more money, and her parents, although proud, were worried about her entering. Makoto passed her examinations, and was soon accepted.  She personally knows Kagura Mutsuki.
Heart to Heart, Remix Heart, The BLUE
One week after meeting Noel and Tsubaki, Makoto met Mai Natsume, becoming interested in her and becoming good friends. She went to the Ars Magus aptitude test which was presided over by Estella McKenzie; her physical abilities were noted to be exceptionally high but her ability to study was low. Makoto told Mai to not eat Noel's dreaded cooking later that evening and watched as she not only went against her advice, but also enjoyed the “death dinner” that had been prepared – soon afterwards, she learnt of Mai's super-taste ability and looked after her after she fainted in the changing rooms. Around this time, she met Kajun Faycott, becoming good friends with her.  The Torifune Festival soon came, and Makoto met Taro Sasaga'e, and Akane Teruhiko. She stole Mai's first kiss, and helped Tsubaki try to win the festival's tournament, being confused when Kajun usurped her glory. 
The girls would soon end up lost in Torifune's lower floors in an attempt to find watermelons. They were choked by a thick cloud of seithr, and sought refuge in a nearby mansion where they were attacked by a mutated watermelon. Makoto, Noel, Tsubaki, and Kajun were saved by Mai, and they found the Evolution Grimoire. Afterwards, they decided to name themselves Team Remix Heart.  Spring cleaning was ordered by Estella days afterwards, and Remix Heart dedicated themselves to cleaning their professor's room, only to discover a hidden room with numerous frilly dresses - Makoto tried some on, giving Noel some bra padding. They discovered the Ammit Cryas Grimoire, handing it over to Estella, but being issued the maximum penalty - a full course of Noel's cooking.  When the time for the sports festival arrived, Makoto led Team Remix Heart with her formidable strength, being protected by Noel and Tsubaki when she was flanked by other participants; the girls discovered that they would have to find the Conversion Grimoire, and journeyed lower into Torifune to do so.  They found themselves in a desert, and Makoto fell into a lion ant pit; she was saved by Mai's quick thinking. The actions of the group earned the praise of the Guardian, who gave them the Conversion Grimoire after a small test, and the girls returned back to the higher levels only to discover that they had come last place. 
Thanks to Taro, Makoto, Remix Heart, and Jin were all sent hurtling towards a beach when Torifune's weather system had broken down. Using Golden Angel supplied by Kajun, Makoto swam in the sea, finding the Regulation Grimoire. The girls fixed it, and restored Torifune's weather.  With Tsubaki, Kajun, and Noel, Makoto found Mai unconscious, being stuck in a dream created by the Hypnagogia Grimoire. She battled against a weak version of Hakumen accidentally created by Tsubaki, and Mai saw a vision of her in the future within the dream before finally waking up.  When Mai lost her memories, the only way to restore them was to taste the tears of those close to her - Makoto supplied her own by crying when yawning, becoming happy with having helped. 
In an attempt to find the Azure Grimoire, Remix Heart travelled to the lower levels of Torifune, and used several Grimoire that they had stolen from the Academy to do so. They cleared a cooking trial, but became separated from Mai when a fissure swallowed her up.  Makoto passed the laundry trial with the remaining girls before finally finding Mai near the Aedsqui Grimoire - they returned to the higher levels.  Makoto learned about Mai becoming the Intermediary Grimoire, and later met Shiori Kirihito and Chachakaka.  She was introduced to the former, falling for her lies of being frail. Jin, Akane, and Taro were bedridden, and Makoto helped to look after them with the other girls.  She watched Noel and Shiori work together to make porridge for the boys, calling out Taro when he ate Jin's and not his own.  She watched as Jin went berserk with his Nox Nyctores - the Mucro Algesco: Yukianesa and as he was knocked out by Cypher Albar.  As she was involved in this incident, Makoto helped watch over the giant icebergs that were created, and cheered on Shiori in a contest for eating shaved ice, also being assaulted by a Torifune panda. 
While having lunch with Team Remix Heart, Carl Clover visited them, and Makoto warned him to not try any of Noel's cooking. She prepared her for her date with Taro, painting her nails for the occasion.  She later berated him for turning up late to Mai's date.  Remix Heart was soon split for survival training, with Makoto being paired with Tsubaki and Noel. They reunited with Shiori, Kajun, and Mai when they found the main body of the mountain jellyfish, and managed to not only defeat it, but come first place in the training exercise.  Mai was knocked unconscious and Makoto helped gather up the strongest Ars Magus users to help save her under Cypher's orders. It was a trap set by Cypher himself, and she and the rest of Team Remix Heart had their Ars Magus aptitude stripped away from them until they were saved by Chachakaka. Makoto learned through the Ammit Cryas that Mai was originally a man.  Mai saved the group from being crushed by an alchemy barrier, and Cypher told them all of his plan to create a Burning Red Grimoire. He briefly battled Mai, and Makoto managed to hug her while the fight had paused, recognizing how hard it was for her living with the secret.  When Mai and Shiori were teleported away by the professor, Makoto listened to Jin and helped to round up the best Ars Magus users in the Academy to foil Cypher's plans - they succeeded.  She spent the rest of her first year messing around, and getting into trouble in her classes with Estella. 
In her second year, Makoto was invited to the 2nd Hierarchical City of Iwatsuchi for Jin's medal ceremony as he had just ended the Ikaruga Civil War. Kagura attempted to flirt with her and the other girls with her (Mai, Noel, and Tsubaki) but she swiftly knocked him out, only to be met by Hibiki Kohaku, who promptly put them to work on preparing the celebration.  Kajun, Mai, and Shiori all disappeared, but Makoto was reunited with them thanks to the efforts of Akane.  She was later seen revising with Noel and Tsubaki over the Nox Nyctores and the Dark War, and Makoto admitted that she did not know too much on either subject. She soon discovered that Noel was to graduate six months early, and she spent the remainder of her time at the Academy with Tsubaki. 
A squirrel beastkin. She comes from the lower levels of the city, but was able to take advantage of her unparalleled physical strength to enroll in the Military Academy. At first, she was bullied for her species and hometown, but with the support from her roommates Noel and Tsubaki, she was able to overcome it. Even though she is currently part of the Novus Orbis Librarium's Intelligence Department, she remains close friends with Noel and Tsubaki and still contacts them.
Makoto once acted as an intelligence agent for the Novus Orbis Librarium. After receiving all sorts of missions, she realized the dangers of the Librarium and defected to Sector Seven. There, she met the lead scientist of Sector Seven, Kokonoe, as well as her subordinate Tager, and now works alongside them. Now, she fights with her best friend Noel to save Tsubaki.
As a month passed after the events in Kagutsuchi, Makoto was on her way to Sector Seven with both Tager and Noel. She managed to get the former to state his frank opinion on Kokonoe to Noel, and learned that their destination had changed to be the 6th Hierarchical City of Yabiko, where they would meet with Kagura. Makoto helped Tager explain who Kagura is to Noel, stunned that her friend knew so little about the Black Knight. When the group arrived in the 7th Hierarchical City of Kazamotsu, they were surrounded by NOL troops.
Makoto, Noel, and Tager woke up in a cell in Yabiko. She attempted to punch her way through its walls, but only hurt her fist by doing so. The three of them were soon taken out of the cell to meet Kagura, although Makoto was less than thrilled about the idea after seeing a woman run out of office, screaming obscenities at him. The Black Knight was having a hangover from a party the previous night, so Makoto gave him some water before proceeding to shout and punch him for his inappropriate behaviour. She punched him again when he suggested that the two had spent a romantic night together. Kokonoe retrieved new outfits for Makoto and Noel, and the two girls went out to explore Yabiko together.
When they returned, Makoto overheard Kokonoe and Kagura discuss possibly having to kill Tsubaki, so she burst into the room, demanding to know what they meant. She learned that Tsubaki was in Ikaruga but was still under the Imperator's control. She then left, grabbing Noel and heading straight for Tsubaki's location. They were nearly stopped by Tager, but he allowed them to go.
In Ibukido, Makoto recalled the events of two months ago where she was saved by Rachel. As she turned around, Tsubaki appeared, acting strangely and calling everyone in the world insects who should dedicate their lives to the Imperator. She lost to her friend, but before Tsubaki could finally arrest her, Kagura arrived with a forged imperial decree, allowing him to take Makoto into custody and save her from her friend. They walked back to the Yabiko NOL branch together, Makoto learning that Noel and various interesting people were waiting there.
The following day, Makoto was present at the large meal cooked by Hibiki, and talked to Noel about Mai and Taro, who neither had seen since graduating. Kokonoe convinced her to eat so she could gather her strength for tomorrow, the day where they would try to save Tsubaki. Later on, Makoto listened to Kagura and Jin's plans for the battle ahead, although she was nervous about having to fight her own friend. That same evening, Noel was attacked by Arakune, and Makoto helped in the attempts to break down her friend's door. When they were successful, Makoto fetched Noel some water and expressed her happiness that nothing bad had happened.
After the Battle of Ragna the Bloodedge, Makoto, Jin, and Noel prepared to free Tsubaki, eventually meeting her in the Colosseum as it was encased in an Eclipse Field. Makoto promised that she would free her friend and the two battled – Makoto won by pushing Tsubaki to her absolute limits, retreating and allowing Noel to Observer her, revealing Izayoi. She then watched as Jin fought against Izayoi, and thought for a brief moment he had been killed by the Immortal Breaker. In truth, he was immune to the attack, and the spell on Tsubaki had been lifted. As she made her way to Makoto and Noel, the three of them reunited, embracing each other and crying as the nightmarish conflict between them ended. She later saved Noel from being hit on by Kagura, stepping on the man as she escorted her friend away.
Receiving orders from Hibiki, Makoto joined Tsubaki with making their way towards the 8th Hierarchical City of Wadatsumi where they faced against Relius, Litchi, Ignis Clover, Nu-13, Carl, and Nirvana. She battled against Litchi, following Bang's command and managed to win against the doctor, although neither took any joy in battling each other. The flow of seithr stopped when Bang was successful in nailing the Rettenjo into Kushinada's Lynchpin; Makoto, Tsubaki, and the recently arrived Valkenhayn defeated the opposing group, but they managed to escape.
Some time after exiting her cell, Makoto found Kokonoe and Celica A. Mercury. Celica and Makoto introduced themselves before Kokonoe ordered Makoto to look after her, warning the girl that Celica had a tendency to disappear with her bad sense of direction. Makoto gave Celica a tour around Yabiko, settling at a small café, ordering a coffee and chestnut parfait. The two grew close over their meal together, but Makoto was soon called away by Kokonoe to assist Tager in a mission.
Makoto's mission had her gather the seithr readings in Yabiko, so she posed as a daughter with Tager as her father. She abused this mission to eat as much food as she could, and asked Tager if he had any family, sadly finding out that he could not remember. Their mission was cut short when Makoto received a call telling her that Relius' female assistant had been seen in Ikaruga. They discovered that the assistant was Litchi and tracked her to Downtown; they agreed to escort her back to the NOL branch where Kokonoe was waiting, and Makoto went ahead of the group. She later found Litchi, Tager, Kagura, Kokonoe, and Hibiki in Kagura's office, leaving her surprised but unaware of the gruelling challenge that they just had against Nu and Azrael. She overheard Kagura say that something was starting.
Later that same evening, Makoto visited Litchi, asking her if she knew what Kagura meant earlier. Litchi did not know but the two theorized until the doctor asked out loud what Kokonoe was thinking, knowing the professor was eavesdropping; Kokonoe then told them that she was unsure of what was happening, but that it did not look good.  With Litchi, Kagura, and Kokonoe, Makoto went to Ibukido again, and learned that Relius was attempting to create a Black Beast – she also learned the true reason why the civil war was started: again, to create a Black Beast.
A squirrel beastkin. She comes from the lower levels of the city, but was able to take advantage of her unparalleled physical strength to enroll in the Military Academy. At first, she was bullied for her species and hometown, but with the support from her roommates Noel and Tsubaki, she was able to overcome it. She is currently part of the Novus Orbis Librarium's Intelligence Department, but...?
With Tager and Hibiki, Makoto listened to an explanation of events that had happened in the last few months from Kagura and Kokonoe. She became confused over Ragna's alliance as he had injured Noel and Jin after he was forced to go berserk by Izanami. She was eventually absorbed into the Embryo, having her memories altered and believing that the date was 12/31/2199, and that Kagura was now the Hero of Ikaruga. 
Inside the Embryo's version of Kagutsuchi, Makoto found Kagura hitting on another woman, so she punched him. She was paired with Noel to find Ragna and capture him , but went on a tangent, meeting Kagura in the Kagutsuchi museum and jammed all radio signals as Hazama was lurking in the area.  Before heading back to her original mission, Relius had found her and began commenting on her soul. Makoto ran, scared of the puppeteer, and found herself in Orient Town. She contacted Kagura to warn him of the man she had just met.  She later heard rumours that Noel had fought the Grim Reaper.  She was later transported to Ikaruga by Nine the Phantom and told to defeat Izanami to claim her piece of the Azure.  She found Tsubaki, but was attacked by her friend as her memories began to confuse her. Makoto managed to repel her and retreated until Tsubaki had regained her composure. 
Makoto was ordered by Kokonoe to detain Ragna, and she found him in Yabiko. They battled, but Makoto lost, and was the first of the chosen to have their desires taken by Ragna's Soul Eater.  She was later deployed to find Naoto Kurogane and to persuade him into the frozen space-time – she succeeded and they landed outside of Ikaruga before venturing to find Noel and the others. 
Naoto and Makoto ran into Es when the demi-human lost her qualification as one of the chosen, and her data was backed up when she rejected the Azure, instead claiming that she wishes to protect the people she loves with her own power, not one she does not understand. She ordered Naoto to run and find the others while Makoto fought Es by herself, being defeated and visited by Amane Nishiki, who came to see her off as she dissolved into seithr. 
In the new world created by Ragna, Makoto is a part of the NOL in an infantry division. Alongside Tsubaki, she visited Noel and Lambda at their church, and had dinner with them, extending an invitation from Kagura for Noel to return to the NOL at any time. 
- BlazBlue: Continuum Shift, Teach Me, Miss Litchi! Episode 1 - Reunion! The three girls from the academy!
- BlazBlue: Remix Heart, Chapter 01
- BlazBlue: Remix Heart, Chapter 02
- BlazBlue: Remix Heart, Chapter 03
- BlazBlue: Remix Heart, Chapter 04
- BlazBlue: Remix Heart, Chapter 05
- BlazBlue: Remix Heart, Chapter 06
- BlazBlue: Remix Heart, Chapter 07
- BlazBlue: Remix Heart, Chapter 08
- BlazBlue: Remix Heart, Chapter 09
- BlazBlue: Remix Heart, Chapter 10
- BlazBlue: Remix Heart, Chapter 11
- BlazBlue: Remix Heart, Chapter 12
- BlazBlue: Remix Heart, Chapter 13
- BlazBlue: Remix Heart, Chapter 14
- BlazBlue: Remix Heart, Chapter 15
- BlazBlue: Remix Heart, Chapter 17
- BlazBlue: Remix Heart, Chapter 18
- BlazBlue: Remix Heart, Chapter 19
- BlazBlue: Remix Heart, Chapter 21
- BlazBlue: Remix Heart, Chapter 22
- BlazBlue: Remix Heart, Chapter 23
- BlazBlue: Remix Heart, Chapter 24
- BlazBlue: Remix Heart, Chapter 25
- BlazBlue: Variable Heart, Chapter 01
- BlazBlue: Variable Heart, Chapter 18
- BlazBlue Material Collection, Noel Vermillion Short Story - The BLUE
- BlazBlue: Continuum Shift Extend Official Site (JP), Makoto Nanaya
- BlazBlue: Chrono Phantasma Official Site (JP), Makoto Nanaya
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 2: Difference of Opinion
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 3: Beneath the Surface
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 4: Kagura Mutsuki
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 6: Friendship
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 9: Izayoi
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 11: The Night Before…”
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 12: Uninvited Guest
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 14: Inherited Will
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 15: The Truth
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 17: Doomsday
- BlazBlue: Chrono Phantasma, Story Mode, Episode 18: Beginning of the End
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 3: The Melancholy of Celica
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 4: The Land of Ikaruga
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 6: Litchi's Determination
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 7: Looming Darkness
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 8: The Forbidden Research
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 9: The Beast
- BlazBlue: Central Fiction Consumer Edition Official Site (JP), Story - Makoto Nanaya
- BlazBlue: Central Fiction, Story Mode, Episode 001, Chapter 002
- BlazBlue: Central Fiction, Story Mode, Episode 002, Chapter 012
- BlazBlue: Central Fiction, Story Mode, Episode 003, Chapter 017
- BlazBlue: Central Fiction, Episode 003, Chapter 018, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 004, Chapter 23
- BlazBlue: Central Fiction, Story Mode, Episode 005, Chapter 036
- BlazBlue: Central Fiction, Story Mode, Episode 006, Chapter 044
- BlazBlue: Central Fiction, Story Mode, Episode 009, Chapter 070
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapter 090
- BlazBlue: Central Fiction, Episode 011, Chapter 092
- BlazBlue: Central Fiction, Story Mode, Episode 012, Chapter 100