Heart to Heart, Remix Heart
At the Academy, Jin met Taro Sasaga'e and Akane Teruhiko, becoming close to both as all three of them were roommates, and all had joined the student council. In his second year, Jin won the Torifune Festival's martial art tournament, becoming its 'Izanagi' for the year. He largely neglected his duties, however.
After having saved the girls from pit they fell into, Jin was seen again in the Torifune Festival of that year. He won the tournament again, this time it being 'rock-paper-scissors'. Jin also introduced Tsubaki to Taro and Akane, having frequently mentioned her in the past. Jin also met Kajun Faycott and Mai Natsume, with the former working alongside him as the 'Izanami' of the year.  Jin also helped judge during the sports festival  and was confused when Team Remix Heart managed to bring back the Conversion Grimoire - he talked to Estella McKenzie about the incident. 
The weather system that manages Torifune eventually broke down, returning the city to its natural state of perpetual cold. Taro accidentally shoved Jin into Team Remix Heart, causing them to slide across the icy pavements until they hit Akane's igloo and were sent careering into the distance, landing at a beach. Jin refused to use the Golden Angel that Kajun had provided, and they waited until they were picked up by Torifune officials. In the meantime, they had fixed the Regulation Grimoire, and brought the weather system online.  Days later, Jin felt Ragna's presence in Torifune. 
Because Taro had kissed Mai, he took on Noel's "death dinner" cooking, sending him, Jin, and Akane into a bedridden state.  Remix Heart, bar Noel, looked after the boys, and Jin joked that Mai couldn't possibly be in love with an "idiot" like Taro. He was introduced to Shiori Kirihito, although he was never made aware that she was an assassin hired by Kisaragi members to kill him.  He was gifted some porridge by the girls, but Taro quickly ate some of it before Jin could even taste it. However, Jin felt Ragna's presence on Mai, and Yukianesa's influence began to take hold.  Hypnotised by the Nox, Jin wildly attacked Mai while Taro attempted to stop his movements. Noel soon arrived, using the Arcus Diabolus: Bolverk to temporarily distract Jin, allowing for Cypher Albar to intervene and knock him unconscious - Jin was carried back to a different dorm, as he had destroyed the one he had been staying in. 
Thanks to the Yukianesa incident, massive icebergs had been created around Torifune, and Jin was ordered to help manage them with everyone else who was involved. He watched Taro battle Shiori in eating shaved ice and was not pleased when a Torifune panda attacked Tsubaki.  While bathing with Taro and Akane, Jin watched as the former was gifted an Ars Magus sealed letter and could not open it. Taro begged for Jin's help, but he refused. 
Jin was soon gathered to help break Mai out of an alchemy induced coma, but he and the other students present were ensnared in the trap laid by Cypher. Taro saved Jin and Akane from the alchemy barrier created , and watched as Mai not only awoke from her coma, but also battled Cypher one-on-one.  When the professor teleported away with Shiori and Mai, Jin took control, ordering everyone present (Taro, Noel, Tsubaki, Kajun, Chachakaka, Estella, and Makoto) to gather all the strongest Ars users to create a barrier of Ars Magus that would stop Cypher's plan of creating a Burning Red Grimoire - he also ordered Akane to evacuate the student body.  They succeeded. Jin was told that Cypher was nowhere to be found after both Mai and Shiori were rescued from the lower levels of Torifune, and he wished to speak with Chachakaka, but she relented. Jin, with the rest of the student council, was then swamped in paperwork surrounding the event. 
Later that year, Jin graduated.
Ikaruga Civil War
Spiral Shift, Variable Heart, Determination
Kagura told Jin about the whereabouts of Meifang within the 11th Hierarchical City of Shinatsu, ordering the Kisaragi heir to arrest her on grounds of treason. He willingly went, travelling to its cauldron and reunited with Mai, also meeting Bell. Upon entering, he froze solid one of the many Fuzzy as snow began to fall in the enclosed space.  He talked to the Colonel, letting her know that he was going to cut her down, remembering the deaths of the Ninth Squadron, Grimwood's execution, and Karenjina's torture. The two began fighting while Mai battled the numerous Fuzzy. Eventually, Mai launched her Legacy Weapon, the Gallia Sphyras: Outseal towards Meifang, puncturing a large hole in her shoulder - Jin followed up by freezing parts of her, yet it was not enough to take the Colonel down. 
Jin lost sight of both Mai and Meifang as the latter created a Phantom Field. The Colonel was defeated and Jin left with Taro pursuing him. He was reunited with Akane and Taro for a brief moment aboard an Ars Magus vessel. 
Not long after his promotion, Jin was given a book called the "Biographies of Heroes". He looked at the book, and felt disdain towards it, mentally remarking that most of his biography had been vastly dramatized; regardless, he signed off a check-sheet to say that the book was acceptable for publishing. Jin was interrupted by Noel, who handed him a letter telling him that she had been placed under his command as his secretary. This greatly annoyed him, and he dismissed her before losing his temper at Yukianesa.
The following day, Noel handed him a letter from NOL headquarters. The letter detailed that Noel was to be deployed to the 13th Hierarchical City of Kagutsuchi and to watch the Grim Reaper - Jin learned here that the Grim Reaper is in fact Ragna the Bloodedge, his long-lost brother. The Major began to maniacally laugh to himself before leaving his office, making his way to Kagutsuchi and abandoning his post. 
A major of the NOL hailing from the Kisaragi family, who earned the title "Hero of Ikaruga" by ending the Ikaruga Civil War. Although he is supposed to be faithful to the NOL, one day he suddenly ignores his orders and heads to the 13th Hierarchical City of Kagutsuchi.
|Stage IV: Bang Shishigami|
Bang: Jin Kisaragi from the Library, I presume?
Jin: Hmm?...Oh, those strange clothes... You must be from Ikaruga. A..."ninja," right? What does a ninja want with me?
Bang: Nuoooooooh! How dare you mock me! My name is Bang Shishigami! Don't tell me you've forgotten this face! I've tried to live my life by my master's last words... But now that I've seen you, I don't think I can do that anymore... Forgive me, Master! My last vow to you... "Don't hate people...hate evil"... I'm afraid I'll have to break it today! I am the protector of Kagutsuchi's soul! I, Bang Shishigami, will not let evil pass by! Haha, I will not miss this opportunity! My master's death will be avenged! Jin Kisaragi! In the name of justice, I must destroy you!
Jin: Do you ever shut up?
Bang: Gugh! Master...I'm...sorry...
Jin: Hmph. What a waste of time.
|Stage VIII: Noel Vermillion|
Noel: Major Kisaragi!
Jin: Oh, it's you. What do you want, Lieutenant Vermillion?
Noel: Major, you've disobeyed a direct order. Headquarters said they will overlook this incident if you return to your post right now. So, sir, please...!
Noel: You're a war hero with a very important position. If you don't go back, you could be tried as a deserter. Your trial would cause an uproar in the Librarium. And...this particular mission was assigned to me. Why are you here in Kagutsuchi, Major...?
Jin: Get out of my way.
Noel: Eh? Major, what are you...?
Jin: Who... Who... Who the hell do you think you are!?
Jin: Why don't you just...go die...?
Noel: S-Stop it...sir...!
Jin: You trash... Scum! Get out of my way! ...Hm?
Jin: Oh, that's where you were...
|Stage IX: Ragna the Bloodedge|
Ragna: Haah... Haah...
Jin: This is an odd place... It's like time has completely stopped.
Ragna: !? You bastard!
Jin: That was pretty harsh, just attacking me like that... Hm? You look injured... Are you OK? It's been a long time, hasn't it? You're reckless as always, Brother.
Ragna: Why the hell are you here, Jin!?
Jin: "Why"? I thought that was obvious: to see you, Brother! ...Heheh...haha...ahahaha!
Ragna: What's so funny!?
Jin: Oh, I'm just happy you're alive... Now I get to kill you again!
Jin: No... Brother, that wasn't fun at all!
Ragna: Damn it... The wounds from that asshole in the mask aren't healing...
Jin: Brother...this isn't enough... I need more than that...
Ragna: You piece of shit...!
Ragna and Jin: !?
|Stage X: Nu-13|
Nu-13: Loading...loading...loading...loading... Complete...
Jin: Who are you?
Nu-13: Scanning: complete. Auto-mode: confirmed.
Jin: Yukianesa is reacting...
Jin: Hurgh... Something's... something's flowing into me... Information? No... these are... memories...
Nu-13: Scanning: complete. IFF determined. Processing... Subject is hostile. Activate termination protocol.
Jin: Oh... I see... So that's what you are... You... are the enemy!
Jin: Gah! What's going on!?
Rachel: Until we meet again. Good-bye, Mr. Hero.
Jin: What!? Where is he!? Brother... Brother...!? You bastard!
Jin: Hmm... This is the only place I can feel relaxed anymore.Trying to act nice around others isn't my forte, and I'm not really good around crowds of people either... Brother... Hm?
Noel: I'm sorry... That's mine...
Jin: Hm? Oh, this? It can get really windy here, so you should be careful. Are you new here?
Noel: Y-Yes... Thank you very much. U-Um... My name is Noel Vermillion... A first year. I joined the Military Academy this year. P-Pleased to meet you.
Jin: I'm Jin Kisaragi, a third year. Nice to meet you. Um... Miss Vermillion, was it? Isn't it a little rude to look at the ground when you greet people?
Noel: Ah! I'm sorry... I'm so sorry!
Noel: U-U-Umm... I'm very sorry, uh, Jin...... but... could you give that back?
Jin: Huh? O-Oh...right. Here you go.
Jin: Who the hell is that girl? Saying they look like twins would be an understatement... That girl looks just like her. Damn. Just when I was beginning to forget... How frustrating.
On the 30th of December, Jin found himself within the district known as Roningai. Here, he was found by Bang, but the major failed to recognize the ninja. Bang attacked in vengeance for Tenjo but Jin defeated him, having used Yukianesa to freeze parts of the district. He refused to kill the ninja, remarking that he was not worth the effort of killing. As he left, Jin began to mutter; each breath dripping with lust for Ragna's death.  The following day after having crossed over most of Kagutsuchi, he came across Noel who had been ordered to apprehend him and bring him back to headquarters. He ran towards her with Yukianesa drawn, swinging at her but barely missing. The two fought, but Noel was saved as Hazama created a smokescreen for her to escape. 
Jin finally made his way inside the Kagutsuchi NOL branch, finding it was empty. He expressed a brief joy for it being so; it would mean no one would interfere with him battling Ragna. Soon enough, his brother arrived, and Jin drew Yukianesa, rushed towards Ragna and clashed against Aramasa. Throughout the fight, Jin's unbridled laughter illuminated the Cathedral, yet he was not strong enough to defeat Ragna. Eventually, Jin was beaten and sent unconscious, his last thoughts being on how cold his hands were. He was found by Noel and Hazama - the latter had him detained on an Ars Magus vessel hovering around Kagutsuchi's airspace. 
As soon as Jin found out about the SS-Rank criminal, Ragna the Bloodedge, he was exhilarated, and filled with nostalgic thoughts of his brother, as well as murderous intent. He immediately made his way to the 13th city of Kagutsuchi on foot, as he sought to avoid being detected by NOL headquarters. As he arrived in the 25th area, Roningai after taking many detours, Jin could feel the presence of many other individuals. Not before long, Bang Shishigami, and a horde of his followers came from hiding, challenging Jin to a fight out of vengence for his Master. Jin claims to be unaware of such event, and does not even remember Bang's face, which angers him, and his followers greatly. Bang tells his followers to stay on standby, as he proceeded to fight Jin alone. Jin makes quick work of the enthusiastic ninja, defeating him with ease. As his subordinates shouted at the Major with aggression, Jin paid them attention, and continued with his travels.
Next, Jin arrived at area 5, Kagutsuchi Port, after taking another detour to avoid detection. He feared that he's running low on time, as many others have been targeting Ragna due to his large bounty, and other personal reasons. In the midst of his thoughts, he was approached by Carl Clover, and his Nox Nyctores Nirvana. Carl notices that Jin is looking for the Grim Reaper, Ragna as well, and states that if Jin were to find him first, it would turn out unfortunate. Jin, seeing this as a threat, provokes Carl to a battle, defeating him without effort. As Carl was grounded, Jin finally remembers him from the Military Academy, claiming that he was disappointed with his choices in becoming a vigilante. Claiming that he's wasted too much time, Jin proceeded to take his leave.
Finally, he arrived at the branch office, however, it was strangely vacant. He searched every single corner of the cathedral for a presence, and found a faint trail. And soon, he was face to face with his lieutenant, Noel Vermillion. Noel came in orders of the NOL, requesting Jin to come back to his position immediately. Her face, and voice both made Jin feel both irritated, and dizzy. Because of her uncanny resemblance, Jin found it difficult to be in her presence, going insane, and attacking her. When he regains his senses, Noel was nowhere to be found. Jin continues deeper inside, arriving at the gate.
There, he found his brother Ragna the Bloodedge. Discarding his aloof, cold personality, Jin became wicked, and murderous upon seeing Ragna. Much to his brother's dismay, Jin began to speak about the days about the church. Laughing hysterically, Jin then begins to engage in a battle with Ragna. Jin manages to defeat Ragna, claiming to have been dreaming about the day he was able to kill Ragna. As he was about to deliver the final blow, the gate began to open, Nu slowly emerging from it.
As Jin and Nu were faced with one another, Ragna warned Jin to stay away from her. Suddenly, memories began to flow into Jin's mind from Yukianesa. Then, Jin begins to go insane, once again, and attacks Nu. All of Jin's efforts were futile, as no matter how many times he strikes, Nu never fell. Nu heavily wounded Jin, and proceeded to walk over to the defeated Ragna. She takes the Grim Reaper, and leaps into the cauldron. Jin, using the rest of the strength in his body, runs after her, desperately calling for his brother. He jumps into the cauldron right after them, disappearing from the timeline along with them.
An Ars Magus of the 4th Thaumaturgist Squadron with the position of major, known as the "Hero of Ikaruga" due to his victories during the Second War of Ars Magus. Despite being treated for injuries from the previous incident, as if being led towards something, he heads for the Kagutsuchi branch of the NOL. 
Transcript of Jin's Continuum Shift arcade.
|Stage IV: Hazama|
Jin: ...Step aside, Captain
Hazama: Oh, you in a hurry? Looking for something, maybe? Would you like some help?
Jin: ... This doesn't concern you.
Hazama: Oh-ho, c'mon now... I was just kidding! You don't need to be such a grumpy-puss. Now turn that frown upside down before you ruin that pretty face, Major Kisaragi.
Jin: ...Ugh!? What...!? What was that?! I thought I saw... Hrg! ...Your face... your voice... You're pissing me off!
Hazama: ... Well that's a little weird. Thought I wiped you pretty clean. Maybe I missed a few bits...
Jin: ... What? What the hell are you talking about!?
Hazama: Hmm... I wonder? What a selfish guy you are. It's all take, take, take with you. Then just toss it aside when you don't need it anymore.
Jin: ... What!?
Hazama: OK, OK, I get it. You want to see Ragna, right? Hoping he'll show up and scold you a bit? Can't depend on your brother all your life, you know! Hahaha!
Jin: Shut up! You bastard!
Jin: ... Die
Jin: Are you insane? You're about to die. What could possibly be funny!?
Hazama: Oh, I'm as sane as the day is long. I just can't believe you're such an idiot.
Hazama: While you're wasting your time yelling at me, things've started happening... The gears are moving, and you're just about the only chump who doesn't know.
Hazama Hmmm... Interesting. More mature? Well, only a little. Still... I -was- going to off you, but maybe I'll... eh heh... help you a little while longer...'
|Stage VIII: Noel Vermillion|
Noel: Major Kisaragi!
Jin: ... Lieutenant Vermillion
Noel: What are you doing here!? Please return to the hospital-
Jin: ... Shut up
Jin: Shut up, Noel Vermillion! Isn't there... something you should be doing? Why are you following me?
Noel: I-It's my m-mission...
Jin: ...Mission!? Hah! That again!
Noel: That's... That's not the only reason. I respect you, as my superior, and... uh... That's why...
Jin: ... That's why?
Noel: I want you to do the right thing, Major.
Jin: Hah. Since when are you important enough to give me orders?
Noel: O-Oh... Oh! I'm sorry! What I meant was... ah... I mean...
Jin: You never change, do you?
Jin: From the time we first met... Huh...? Ugh...! What is this!? Yukianesa? Ugh - Aaaaagghh!
Jin: Die. You're in my way!
Jin: *Pant* *Pant* Don't ever... Show your face before me... again...
Noel: M-Major Kisaragi...
<Jin leaves, Noel collapses>
Hazama: Ah, just what I'd expect from a hero. Like old times, eh? Such determination! Won't get you what you want, though. Almost painful to watch... But hey, you did save me a lotta time, so... I'll just be taking her now...
|Stage IX: Tsubaki Yayoi|
Jin: That uniform... Squad Zero, the Wings of Justice, huh? Who the hell are you?
Jin: ... Tsubaki?
Tsubaki: I'm sure you already know why I am here, Jin...
Jin: Tsubaki... I never thought you would become one of the Wings of Justice, unsurprising though it may be. No matter. Do you know what that thing in your hand is?
Tsubaki: ... The Armagus Izayoi.
Jin: A cursed weapon that steals the light away from the one who wields it... Don't tell me you've already-!
Tsubaki: Jin... Are you actually concerned for me...?
Jin: That's not important, Tsubaki! Why do you have something so dangerous-
Tsubaki: There is still time. Even if I lose the light of day, the truth within my heart will never fade. My own truth will always guide me.
Jin: Truth...? This world is nothing but corruption, treachery, and lies. What meaning is there in "truth"?
Tsubaki: You always hated lies, Jin... Is that still how you feel?
Jin: Yes. Absolutely. Trust, love, respect, hate, jealousy... Nothing more than lies. The only truth in this world is death.
Tsubaki: Then I suppose you will never know the pain of those who must lie...
Tsubaki: Please go back to the Librarium, Jin. Otherwise, I will be forced to...
Jin: No. You have delayed me long enough.
Tsubaki: I can't change your mind...?
Jin: No. You cannot.
Tsubaki: I do not wish to kill you, Jin.
Jin: You must be kidding... Do you really think you pose any threat to me?
Tsubaki That is why I have Izayoi, Jin... The least I can do for you is deliver your judgement with my own hands.
Tsubaki: Jin... No. You mustn't... go...!
Jin: Tsubaki, your eyes... They... I'm sorry, but I must see this through to the end. You should return to base.
|Stage X: Ragna the Bloodedge|
Ragna: Outta my way, Jin. Whether I go through you or past you is your choice.
Jin: You're not going anywhere, Brother. No! Not... again... Stop giving me orders, Yukianesa! Gugh... ugh, argh... Shut up! Shut up, shut up, SHUT UP, SHUT UP!
Ragna: Jin, you!
Jin: Ha... haha... I beat it, Brother! At last! That damn Order that's been crowding my head for so long! Gone! Ah ha! Aha ha ha ha ha!
Ragna: The Power of Order? Then... you're resistant! That son of a bitch... He knew that, and he chose to use you...!
Jin: Ahahaha! Brother, why does that even matter!? Yukianesa and the Power of Order were only the beginning! All that is in the past now! You and I are the only two who exist right now, Brother! I... I can finally kill you! My choice! Mine! Finally... FINALLY we can have some fun!
Ragna: ... Oh man, you really lost it this time, idiot! Wake up!
Jin: Oh, does it hurt? Ha! What am I saying!? Of course it does! Don't worry, Brother... I'll put you out of your misery, right NOW!
<Hazama strikes Ragna>
Hazama: Wow guys, you have got some serious Cain and Abel shit here! Think you've worked that out of your system yet, Major Kisaragi?
Ragna: Dammit... Terumi...!
Hazama: Oh, calm down. I made sure to miss all your really important bits. Besides, it's not like good old Ragna'll die that easy. He's built good 'n tough!
Jin: ... You bastard!
Hazama: Wh-Whoa there! I saved the best seats in the house for you two... The real show's about to start. If you start acting up, I'm gonna have to kick you out.
Jin: Captain Hazama... What are you plotting?
Hazama: So many wannabes up on the stage these days... Made my job real tough, you know. I just want to make sure I'm 100% crystal clear on this... You guys are the audience. You ain't gonna set foot on this stage, no matter how hard you try. Yeah, not even as extras...
Hazama: And you, it gives me great pleasure to introduce our leading actress!
Hazama: Will everyone please give a warm welcome to Miss Noel Vermillion!
Jin: Noel... Vermillion...?
Hazama: Ladies and gentlemen! Our stage is set! Let the ultimate show BEGIN!
Although praised as the Hero of Ikaruga, Jin Kisaragi has split from the NOL due to certain events. Released from Yukianesa's curse through the Power of Order and having received Jubei's teachings, Jin heads towards Ikaruga.
During his training with Jubei, Jin was told about the Amaterasu Unit and the Boundary Interface Prime Field Devices. He also learned about the Izayoi, but was told to find Hakumen if he wanted to learn more. After his training ended, Jin made his way to the Ikaruga Region again, this time arriving in the 9th Hierarchical City of Akitsu-Ko. As he stood in Snow Town, he knew that Ragna was also in Ikargua, but prioritized saving Tsubaki from the NOL first. Before he could proceed, he was found by Hibiki, who tried to convince him to help with Kagura's coup d'etat. Jin was approached as he was the next head of the Kisaragi's, while both the Yayoi's and the Hazuki's had yet to be asked. Hibiki stayed with Jin to try and convince him to come back to Yabiko; they first went to the cauldron, Jin being curious over its state after learning from the secretary that Ragna had destroyed it.
When they arrived at the cauldron, Hibiki told Jin that its functions had completely stopped. Jin ordered Hibiki to stay back, and he went further into the facility, finding Relius Clover blocking his path. Before the Mad Puppeteer left, Jin blocked him and the two fought, although Jin was bested by an unknown technique that Relius employed. Hibiki rushed to the Major's side, narrowly missing meeting Relius. The two decided to go back to Kagura.
As soon as Jin entered Kagura's office, he was playfully mocked by the Black Knight, who referenced his nickname in the academy that Taro had given him. After listening to Kagura and Kokonoe's plans to have Tsubaki lured to the Colosseum, he decided his time was better spent trying to find Hakumen than sitting around. He used Order to make Hakumen come to Snow Town and duelled the hero, recognizing that he was an alternate version of Jin himself. After the battle Jin asked for information on Izayoi, learning that it had another form that could kill immortals, the Zero-Type Izayoi, and also learned that Hakumen was indeed Jin from another phase, although he was not sure which one.
When Jin returned to Yabiko, he entered Kagura's office. Ragna was there, but he initially ignored him, focusing his attention on Kagura, who told him that they had moved the plan to be happening sooner since Tsubaki was close to being consumed by Mind Eater. After learning this, Jin turned and headbutted Ragna, the two of them talking down to one another until Noel finally arrived to the office. Jin left when she arrived, telling his brother that he would be waiting for him in the branch's basement.
At the Yggdrasil Seed, Jin waited. Ragna finally arrived and the two battled, but Ragna was in no state to fight properly, and Jin's training with Jubei had made him much stronger. Celica arrived and stopped the two from fighting, putting both of them in their spot and healing their wounds. Both boys were reminded greatly of the Sister.  He was present for the meal prepared by Hibiki the following day, although he was noticeably agitated and asked Celica to not be so familiar around him. After listening to Kagura, Jin knew he had to rely on both Makoto and Noel to help him free Tsubaki from Izanami's grip, so he talked to the two women afterwards, forming a plan for the following day. He was woken that night by Arakune's assault, but apparently did not care much for what had happened. 
Noel, Jin, and Makoto walked into the Colosseum, waiting for Tsubaki. When she arrived, the Eclipse Field activated, stopping anyone from Observing what would happen within. Jin watched as Makoto and Noel followed the plan, seeing Tsubaki become Izayoi. He battled her before taking a blow from the Immortal Breaker, snapping Tsubaki out of her trance as she believed she had killed him. In reality, the ability did not affect him because of the Power of Order. Tsubaki stood back and then hugged him, their nightmare was over for now and the two reconciled. Kagura arrived and told them both that he planned to change the government and overthrow the Imperator, introducing the two of them to Homura Amanohokosaka after hearing their qualms. Jin later overheard a conversation between Noel and Ragna about family, but when the latter called him out for eavesdropping, Jin joined the conversation. The argument between the brothers was cut short as Noel broke it, telling them that they did have to ruin such a great day.  The next day, Jin was called into Kagura's office with Tsubaki and he clashed with Valkenhayn and Rachel, asking why they were both there. After cooling off, Jin received orders from Kagura to guard Homura.
While guarding Homura with Tsubaki, Kagura, and Hibiki, they learned that the group sent to the Lynchpin were under attack from Relius. Jin and Homura convinced Tsubaki to leave to help them, but as she left, they were attacked by Izanami and Phantom. Although the men tried to fight back, Phantom stopped their movement. He witnessed as Izanami abdicated her position as Imperator, handing it to Homura.
Jin escaped from Yabiko and met with Ragna and Noel, and together they witnessed the Gigant: Take-Mikazuchi fall from space and onto the planet. They decided to work together, going ahead and attacking the monster while it was weakened by Celica's presence. After battling Izanami and Take-Mikazuchi, Jin left to the base of the Monolith where he helped destroy alongside Hakumen, both using "Winter's Reposte" to do so. When he came back, he saw that the flow of seithr had stopped. Izanami sent Ragna berserk and Jin was forced to fight against his brother alongside Noel. Unfortunately, he was given mortal wounds from the battle. Celica's healing only did so much, but she repeatedly gave her best for him.
Jin made his way to the 8th Hierarchical City of Wadatsumi, a location he had not visited since the civil war. Bang found him and the two fought, although Jin could feel the presence of the Imperator throughout Ikaruga and cared little about the battle he was supposed to be engaged in. In the end, Bang fell through a hole thanks to his own technique and Jin continued on his own way.
A captain of the NOL, from the famous Kisaragi family. Although he was supposed to be faithful to the NOL, one day he suddenly ignored his orders and left for the 13th Hierarchical City of Kagutsuchi. Only he remembers that he once held the title of Major and was hailed as the "Hero of Ikaruga."
The fight against Ragna had seriously injured Jin and he had no recollection of it afterword. He was unable to move, and even Celica's healing sorcery was not enough to heal his wounds. Celica left after some time, and Tsubaki visited him. He explained his relationship with Ragna, and his earliest memories to her, including the day he cut Ragna's arm off under Terumi's influence. They were interrupted by Noel, whom Jin had sent for earlier, and Tsubaki left. Noel told him what happened in the fight, and he ordered her to find Ragna before Tsubaki would. Trinity Glassfille was watching, and he spoke to her after Noel had left; they formed a pact, and Trinity, using alchemy, made his body able to fight again, although at the cost of him being unable to ever fight afterwards. Jin was later absorbed into the Embryo but the Power of Order prevented his memories from being altered. 
Part of his pact with Trinity was to find Platinum the Trinity, which he attempted to do inside the Embryo. He found his way to the Monorail in Kagutsuchi.  Much later on, he would find Jubei, and they discussed the latter's distorted memories. Jin left his mentor to go and investigate the strange world they were in.  He was teleported to Ikaruga by Nine, and instructed to defeat Izanami to claim a part of the Azure. Jin trusted Trinity's instinct to go to Kokonoe to complete both their goals. 
With barely any time left, Jin and Trinity found Platinum, whose existence was on the verge of disappearing. He perceived both Luna and Sena, recognizing them with the Power of Order. The measure was only temporary, so Jin resolved to help Trinity make it permanent.  The three of them broke into a Sector Seven facility and escaped with information pertaining to Platinum's body.  He allowed Carl to help Trinity with modifying Platinum's body so they could exist within the Embryo. 
After finishing the maintenance and saving Platinum, the trio left Carl and were found by Jubei, who warned them of the eleventh Nox Nyctores.  They travelled to the Kaka Village first to drop off Platinum so she could materialise the Hihiirokane, which Jin concluded could outright kill Terumi.  Later, Jin travelled with him to Yabiko where they found Celica, Noel, Ragna, Kokonoe, Kagura, and Rachel discussing how to break into Nine's workshop. He told Kokonoe it was impossible to naturally enter the workshop.  The following morning, Jin was part of the strike squadron sent to Nine's workshop. There, he listened to Nine's explanation of the world, the Prime Field War, her desire, and why she created the Corpus Sepulcro: Requiem. Although he believed her a threat to Order, he could not attack her because it would drain his body far too much.  He watched Ragna defeat the sage, and attempted to fight off both Izanami and Nu, who had come to kill them all. He could not fully fight, however, and was teleported away after watching Nine die to delay Doomsday and stop Izanami from moving for a week – he was also forced to leave Jubei behind. 
Jin and the others were teleported to the church that he grew up in, leaving him shocked as to how it could exist, even within the Embryo. While the others went inside, Jin and Ragna talked about how it could possibly exist before deciding to go to the nearby river – both completely calm and not at one another's throats.  They returned to the church to sleep, and had breakfast together with Celica and Noel. He left the building and talked with Rachel, Trinity, and Ragna about the situation at hand and agreed to “play house” for the time being.  Jin also listened to Noel perfectly describe his childhood through Saya's eyes, calling it “impossible”.  The hero later listened to Trinity's request to stay inside Yukianesa so she could help him to defeat Izanami and Terumi, and he complied. The following morning, he watched Celica finally die, and the group teleported back to Yabiko – it's unknown how her death affected Jin. 
Jin would be reunited with Tsubaki, Kagura, and Kokonoe back at the Yabiko branch, and also met Hakumen. He listened to Noel, learning that she holds one half of Saya's soul, and agreed to be sent within the Embryo's frozen space-time to deal with Requiem and Izanami, being taken there by Lambda-11.  Inside, he was separated from the others, being stranded with Kagura. They were found by Azrael, who shifted space-time to fight them in the Colosseum. After watching Kagura fight the Mad Dog to a near stalemate, Jin intervened, using "Artic Dungeon" to freeze him, and the two became the first pair to ever defeat Azrael. Jin left Kagura behind to rest and travelled onwards to find Requiem. 
The final part of Doomsday began to occur, leaving Jin and Trinity stranded in the White of Nothingness. They soon ventured to find the others and Amaterasu. He eventually did, finding Tsubaki, in her Izayoi form, alongside Hakumen battling Nu. He watched Ragna defeat both Nu and Hakumen, and then Terumi breaking Hakumen's soul and taking the Susano'o Unit for himself, becoming Susano'o once more. Jin watched him snatch Noel and transport both himself and the Amaterasu Unit outside of the Embryo. He learnt from Trinity how to escape the Embryo to follow them and journeyed with Ragna to the Kagutsuchi cauldron to do so.  There, he saw Hazama jump into the Boundary and found Rachel. With Ragna, Trinity, and Rachel, Jin jumped into the cauldron, ending up on the exterior of the Embryo. 
Outside the Embryo, Jin and Ragna fought against Susano'o, although the hero had reached the limits of his body after perceiving the God using Order. Ragna dragged Terumi out of the Unit, and Trinity transferred him into the Susano'o Unit with Hihiirokane, and he slashed down both his brother and the God, although both were dragged into the Gate.  Terumi was killed by the Grim Reaper, and when Ragna exited the Gate, he fought against both Jin and Noel, taking their dreams. Trinity took Jin out of the Susano'o Unit. Jin began crying into his brother's arms, knowing this would be the last time he would ever see him. Together with Noel, who had now reclaimed all of Saya's memories, they returned to seithr. 
In the new world created by Ragna, Jin forgot about his brother, and was last seen at an NOL ceremony where Homura presided – both Kagura and Hibiki were also present.  True to Trinity's deal, Jin is now incapable of ever fighting again in his life. 
- BlazBlue: Remix Heart, Chapter 02
- BlazBlue: Remix Heart, Chapter 05
- BlazBlue: Remix Heart, Chapter 06
- BlazBlue: Remix Heart, Chapter 07
- BlazBlue: Remix Heart, Chapter 10
- 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 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 16
- BlazBlue: Variable Heart, Chapter 17
- BlazBlue: Variable Heart, Chapter 18
- BlazBlue Material Collection, Jin Kisaragi Short Story - purgatory hell
- BlazBlue: Calamity Trigger Official Site, Jin Kisaragi
- BlazBlue: Calamity Trigger - Part 2, Chapter 2 - Cross Fate
- BlazBlue: Calamity Trigger - Part 2, Chapter 3 - False Hero
- BlazBlue: Calamity Trigger - Part 2, Chapter 4 - Memorable Church
- BlazBlue: Continuum Shift Extend Official Site (JP), Jin Kisaragi
- BlazBlue: Chrono Phantasma Official Site (JP), Jin Kisaragi
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 3: Beneath the Surface
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 5: The Guided
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 9: Izayoi
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 10: Brothers
- 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 16: Kushinada's Lynchpin
- 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, Epilogue
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 5: The Ninja and Mercenary
- BlazBlue: Central Fiction Consumer Edition Official Site (JP), Story - Jin Kisaragi
- BlazBlue: Central Fiction, Story Mode, Episode 001, Chapter 003
- BlazBlue: Central Fiction, Story Mode, Episode 003, Chapter 015
- BlazBlue: Central Fiction, Story Mode, Episode 004, Chapter 025
- BlazBlue: Central Fiction, Story Mode, Episode 005, Chapter 037
- BlazBlue: Central Fiction, Story Mode, Episode 009, Chapter 064, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 009, Chapter 073, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 009, Chapter 073, Sub Scenario 2
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 077, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 078, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 079
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 081
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 082
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 083
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 084
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 085
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 087
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapters 088 – 089
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapter 090
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapter 092
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapter 094
- BlazBlue: Central Fiction, Story Mode, Episode 012, Chapter 096
- BlazBlue: Central Fiction, Story Mode, Episode 012, Chapter 098
- BlazBlue: Central Fiction, Story Mode, Episode 012, Chapter 100
- Inside-Games, Interview with Toshimichi Mori