Jubei was born to a small beastkin clan in the depths of Japan's mountains. His birth name was Mitsuyoshi. He has two younger brothers - Tomonori and Munefuyu, and came into the service of Clavis Alucard. When the Dark War began, Mitsuyoshi and his brothers survived the advent of the Black Beast, escaping Japan to a different country; their homeland was destroyed by the United Nations as they launched a barrage of nuclear attacks on Japan in a vain attempt to kill it. During their migration, the brothers and the rest of the survivors took the Hihiirokane, a sacred blade passed through their generations. Many of Mitsuyoshi's brethren died fighting against the Beast.
An unknown country offered Mitsuyoshi the chance to use his incredible genes to create an entirely new species that could combat the Beast. He agreed and the Kaka were created. The brothers also came across half-beastkin and gave them a home in their new village. Clavis gave Mitsuyoshi the mission to investigate Relius Clover.
Phase 0, Phase Shift 1, Phase Shift 2, Phase Shift 3, Phase Shift 4
Mitsuyoshi watched as Tomonori ventured into an underground room in their hidden village. Following, he saw his brother grab the Hihiirokane, but the older brother did not chastise him. Mitsuyoshi calmly asked what he was planning to do with it, knowing that the sword was seen as a glimmer of hope among the survivors of the clan. Tomonori answered he was going to use it to cut down his targets, Kazuma Kval and Yuuki Terumi.
He let his brother go, telling him to strike down his target without fail, although he was concerned that Tomonori was not bringing anyone to help in his mission. This was the last time Mitsuyoshi ever saw his younger brother, as Tomonori was viciously murdered by Kazuma.
With Nine and Valkenhayn, Jubei went to the Alucard Castle after Clavis' death. They went to the prison at the bottom of the castle and found Terumi within the body of Kazuma, Tomonori's killer. With Mind Eater being applied to him.
Ikaruga Civil War
In 2192, early on in the civil war, Jubei discovered that the church had been attacked, burned down to ash by Terumi. Celica was dead, Saya and Jin had been kidnapped, and Ragna was the new owner of the Azure Grimoire, the corpse of the Black Beast itself. Rachel told Jubei of the situation, and the old beastkin decided to take him under his wing, raising and training Ragna. Two years into this training, Jubei accidentally sent his pupil meters into the air. Jubei taught Ragna history, how to survive outside of the Hierarchical Cities, how to fight, how to cook, and how to use the Azure Grimoire. He soon learned that Saya had disappeared into the NOL, and that Jin had been adopted by the Kisaragi family, relaying this information back to Ragna. 
Jubei did not participate during the second war of Ars Magus, and instead relinquished his time to training Ragna. One exercise included sending his pupil to the 15th Hierarchical City of Torifune and to take-out the Aedsqui Grimoire. Unfortunately, Ragna failed to do so.  Jubei had the difficult task of stopping his pupil from attacking the NOL, but eventually, a time came when he believed Ragna had finished his training. Rachel and Jubei gave Ragna the red jacket and Aramasa that had formerly belonged to Bloodedge.
In 2198, after the end of the war, Jubei infiltrated an NOL train destined towards the 13th Hierarchical City of Kagutsuchi with the intent of finding the Boundary Interface Prime Field Device that lay within. He caused an explosion, distracting the soldiers on board and fought them with Mai Natsume and Kajun Faycott, who had also infiltrated the train. Mai assaulted him after being controlled by her Legacy Weapon - the Gallia Sphyras: Outseal. After making her calm down, Jubei used Musashi to cut down an Anti-Demon Beast Grimoire that had been launched towards him by a soldier, but the grimoire malfunctioned and the train was sent derailing.  He later rendezvoused with Rachel and Valkenhayn in the 11th Hierarchical City of Shinatsu, finding that the Prime Field he was meant to find had gained an identity as Bell. Ragna had an outburst towards his master and the vampire, but was teleported away. 
After the defeat of Meifang at the hands of Mai and Jin, Jubei met again with Trinity, this time her soul residing inside the body that belonged to Bell, the consciousness of its previous personality no longer within. The two talked about the fairness of the situation on Bell, but Trinity knew it was her wish for the event to happen like it did. 
Once one of the "Six Heroes" that defeated the Black Beast, and a beastkin bearing the nickname "One-Eyed Lotus". He taught Ragna how to use a sword, and was the one who saved Ragna and his siblings and brought them to the "Church." Always one to settle things by himself, he quickly raises the Causality Weapon "Mucro Somnio: Musashi" in order to stop his resurrected wife "Nine." 
Act 3: The Replacement Blue
|Stage 3: Ragna the Bloodedge|
Ragna: Wha-!? Master?
Jubei: Ah, it's you.
Ragna: Don't "it's you" me. What are you doing here!?
Jubei: ...Yes, I suppose you would do just fine. Ragna, think fast.
Ragna: Huh!? Wha-! Wai-!
Jubei: I'd say that should about do it. Forgive me, but you were perfect to test how much I've recovered.
Ragna: Damn that hurt. You couldn't tell me this BEFORE you started attacking me!? You're one crazy cat. Heh, see what I did there? *Ahem* Never mind. I was actually looking for you, too.
Jubei: You don't say.
Ragna: Whatever. Tell me. You don't really intend to fight in that state, do you?
Jubei: Hahaha! Never thought I'd live to see the day you worried about me! Don't you worry. I may have a few scratches here 'n there, but it's not going to stop me from fighting. It's time I settled this score.
Ragna: That's not what I was talking about. But if you've made up your mind, guess there's no point in trying to change it. I've got no intention of stopping you.
|Stage 6: Celica A. Mercury|
Jubei: Hm...? Where is this...?
Celica: Mister Jubei! *pant pant* I finally found you... I was looking all over for you. And boy, do I mean all over. We ran into this huge alligator in a swamp! And it's mouth was HUGE! But, Minerva knocked out all of its teeth, and he swam away crying...
Jubei: I sympathize with you, poor alligator. You didn't see it coming. Never mind that, Celica. Let's set aside your adventure for the moment. You said somethin' about looking for me? As much as I'd love to stick around and chit-chat, I'm in a bit of a hurry.
Celica: You're talking about my sister, aren't you? Mister Jubei. You know that in your current state, you're...
Jubei: ...I'm what? Hah! I hope you weren't looking for me just to tell me that, missy.
Celica: And if I said that I was... ...what are you going to do?
Jubei: ...Nice try. But, you can't stop me.
Celica: You stubborn old man! Get him Minerva. Stop this idiot!
Jubei: ...Hmph. What are you up to, Kokonoe?
|Stage 7: Kokonoe|
Kokonoe: I was trying to show some idiot the truth. Or did you not even realize?
Jubei: ...What?JBCome now. I know it's been a while, but I'm still your daddy. Don't go around callin' me an idiot.
Kokonoe: My goodness, it remembers. I was beginning to think you forgot we were related.
Jubei: Now you've gone too far! I never thought you'd try to throw Celica at me. Illusion or not.
Kokonoe: Interesting. "That" looked like Celica to you? Well then, how about now?
Jubei: ...Kokonoe, I've had about enough of...
Kokonoe: I knew it. Bring everything you've got, you dimwitted father!
Jubei: Wha-!? Kokonoe, we've been in your space all along? Since when was I here?
Kokonoe: The moment you saw Celica. *Sigh* I had a hunch when I saw you fighting Ragna. But, do you get my point now? You're weak. Sure, when you were younger, you could cross the Boundary without batting an eye, but now you couldn't even see through this level of intervention.
Kokonoe: Let me be frank. Even the biggest miracle in the world couldn't help you defeat mother.
Nine: Aww, how kind of you, Kokonoe. Are you that worried about your father?
Kokonoe: Mother!? How did you intervene into my Space?
Nine: Hehehe, it was quite easy. I helped design it, remember? Besides, you really didn't do a great job at keeping people out, Kokonoe.
|Stage 8: Nine the Phantom|
Jubei: What's the meaning of this, Nine...!?
Nine: Do you remember this place? Because I still do. The first time we fought each other. You were very strong. Even stronger than me... Strong enough to defeat Hakumen.
Jubei: What are you getting at?
Nine: You've gone soft. Holding back because she's your own daughter?
Jubei: Of course. I would never dare try to kill her. I would never unleash my strength against an opponent who wasn't trying to kill me.
Nine: Oh? Then I wonder what you intend to do with all that pent up rage you have dormant inside of you. Say, dearest. It's time to see how serious you really are?
Nine: What's the matter, dear? This should be easy for you. Just move your blade to the side, and you can put an end to everything. Hehehe.
Jubei: Everything...? EVERYTHING!? All I wanted to do... Is protect you. That's why I...
Nine: ...tried to bear the sins of all six of us? And continued fighting?
Nine: Oh you haven't changed one bit, have you...?
Nine: You're SOFT!
Nine: That's not good enough! You can't change anything with that. It's time to reset our history. This era. With our own hands! We are going to rebuild this world's system...
Jubei: That's why you want to create a god, Nine!? What reason do you have to deny everything we've done!?
Nine: Reason? Don't make me laugh. I don't expect anyone to understand. I will see my justice through. And, so should you... ...even if that means "killing" me.
Becoming one of the chosen, Jubei was absorbed into the Embryo, and his memories were altered to make him believe that the date was 12/31/2199, as well as other certain discrepancies. He found Ragna on the edge of Kagutsuchi, and warned him about his huge bounty before realising that his former pupil had lost all of his memory, not even recognising his old master. This startled the old beastkin, who had now realised that something was definitely wrong with the world he was in. He left Ragna a cryptic hint to head towards Kagutsuchi before going to do his own investigation. 
In Orient Town, Jubei found Jin, and was greeted as if they had spoken recently, although to Jubei’s memories, he had spoken to him over ten years prior. They both departed on separate ways to conduct more investigations on the world. 
Jubei’s memories returned to him and he found Jin, Trinity, and Platinum, warning them of the eleventh Nox Nyctores, and asking them to return to Yabiko with him since Kokonoe would need all the help she could get. . Before travelling to Yabiko, they dropped Platinum off at the Kaka Village. Totokaka looked at Jubei’s wounds, knowing them to be serious but he shrugged away her concern. He later told Platinum to materialise Hihiirokane so they could cut at Terumi’s soul, lending them the Sekkigan in order to do so since they had never seen the blade.  Trinity, Jubei, and Jin travelled back to Yabiko and met with Kokonoe, Ragna, Celica, Kagura Mutsuki and Rachel. The beastkin revealed how that the entrance to Nine’s workshop is near impenetrable, and that there are specific locks that need to be opened to enter it. Prime Field War, her desire, the world, and why she created the Corpus Sepulcro: Requiem. He watched as Ragna defeated his wife, and ran to her side afterwards.  Izanami arrived and threatened to kill them all, with Nu accompanying her. Jubei protected Nine from the onslaught of Nu’s attacks while Nine, using the Radiance of Extinguishment, was able to briefly bind Izanami and activate Requiem, freezing time. He protected his wife until her last moments, promising to meet her again in the afterlife. Instead of leaving the workshop, he stayed to battle Nu and ensure Requiem was safe so Nine’s death would not be in vain. 
Nu and Jubei found themselves awakening outside the Amaterasu Unit and the old beastkin gave his best to prevent her from attacking the Master Unit despite his grievous wounds. Hakumen and Tsubaki arrived to help him, granting him rest from the weary battle. He talked to his daughter over a communications device, immediately realizing that it was a data copy, and not the real Kokonoe who had returned to seithr. He apologized for being a terrible parent to her, but the copy asked that he instead tell that to his real daughter when the chance presents itself. He looked after Nu alongside Tsubaki until he dissolved into seithr as well, he data backed up by Es. 
Jubei was last seen in the new world created by Ragna, watching over Platinum as she was taken into Litchi’s care. 
- BlazBlue: Phase Shift 1, Chapter 4 - Doubt of Yellow Equilibrium
- BlazBlue: Phase Shift 1, Chapter 6 - Voice of Emerald Evil
- BlazBlue: Phase Shift 1, Prologue
- BlazBlue: Calamity Trigger - Part 2, Chapter 3 - False Hero
- BlazBlue: Remix Heart, Chapter 11
- BlazBlue: Variable Heart, Chapter 04
- BlazBlue: Variable Heart, Chapter 11
- BlazBlue: Variable Heart, Chapter 18
- BlazBlue: Central Fiction Consumer Edition Official Site (JP), Story - Jubei
- BlazBlue: Central Fiction, Story Mode, Episode 001, Chapter 007
- BlazBlue: Central Fiction, Story Mode, Episode 004, Chapter 025
- 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 011, Chapter 092
- BlazBlue: Central Fiction, Story Mode, Episode 012, Chapter 100