At some point, Kyudai theorized the "Quirk Singularity", according to which as the generations pass, the Quirks will become so powerful that they will be uncontrollable. No one, except All For One, believed his theory. At some point, he started working for All For One.
Sometime later, All For One found a discarded boy named Tenko on the streets, after having gone through the traumatic event of killing his family when his Quirk Decay manifested for the first time. At his master's request, he brought for several sets of hands belonging to the boy's family who were accidentally slaughtered when the boy's Quirk manifested. Kyudai watched as the boy started experiencing episodes from recalling the events. Kyudai questioned All For One if he should modify Tenko, but All For One declined and stated that he will teach him how to take his feelings and frustrations and give them purpose.
While Tomura was reporting of his mission's failure of killing All Might, Kyudai expresses annoyance at his Nomu being defeated before All For One calms him since they've found something intriguing about All Might's students.
All For One is surprised that the Hero Killer Stain was captured but is still happy that things are going as he has foreseen. He exclaims that Tomura's position is to supervise and unify the new villains who have come to join the League of Villains. Kyudai expresses doubt that Tomura can do his job and says that if All For One stepped in things would be proceeding faster. All For One asks him to patch him up faster. All For One says that he will let Tomura do all the hard work so that he may become his successor as Tomura was born to do so.
After Endeavor and Hawks' fight with the Nomus, High-End, Dabi confronts the two heroes and initiates a fight with them. He is interrupted by Mirko, prompting Dabi to retreat by asking Kyudai for help. Kyudai has Dabi warped away.
A month prior to the Hero Billboard Chart JP event, the League of Villains were facing Gigantomachia. As they were struggling against the behemoth, Kyudai contacts them from the radio that Gigantomachia is wearing, as he implies Tomura's uncertainty in the League's current state and need for help. Tomura was shocked to hear his voice.
Kyudai asks Tomura Shigaraki if he's keeping his remaining allies healthy, in which the latter admits that the League is running short on members. However, A sad tearful Gigantomachia proceeds to destroy a majority of the landscape, Kyudai introduces more info on Gigantomachia to the League, explaining that he once served as All For One's bodyguard. The doctor points out that the colossal beast possesses unlimited stamina and capable of welding multiple Quirks without any complex modifications. The doctor adds on that as All For One's power began to wither away thanks to All Might, the megalomaniac knew that he'll eventually meet his defeat, thus leading to him hiding Gigantomachia from the public eye.
Before Gigantomachia prepares to unleash another one of his devastating attacks, Kyudai plays a voice recording of All For One from the radio that effectively calms Gigantomachia as he cuddles up to the voice of his "beloved" master. An irritated Tomura claims that he doesn't want to handle Gigantomachia. The doctor tells the young pupil that he spent too much time with Kurogiri and tells him to grow up. Suddenly, black ooze emerges from the League's bodies, transporting them all to a secret laboratory filled with multiple Nomu hybrids.
It is revealed that the doctor was responsible behind the Warping Quirk once used by All For One from the Kamino Incident. He reveals that All For One did this just to make sure his legacy would live on through Tomura's command. The Doctor calls them High-End and says they're much more advanced than the old Nomu. Tomura asks if the Doctor if he can duplicate the Quirk-Destroying Bullets.
In Kyudai's lab, Mr. Compress says that he can't see the Doctor and this spooks the latter into hiding in a dark tunnel. The Doctor apologizes and explains that they are not to approach him unless they want to be transported back to Gigantomachia. He introduces himself as Daruma Ujiko, an admitted alias. Kyudai tells Tomura that he's only helping out of loyalty to All For One. He claims Tomura himself hasn't accomplished anything and he that must prove that he can carry on All For One's will.
Kyudai listens when Tomura confesses that he felt empty before meeting All For One and that the hands he wears on his person make him feel both nauseous and at peace, yet his heart feels heavy which causes his rage. However, Tomura explains that it's this juxtaposition of feelings that makes him hate everything and want to destroy everything. Tomura tells Kyudai that he will show heaven and hell if he will help. Amused, Kyudai responds that it's a childish dream but is impressed by how serious Tomura is in his dream. Kyudai agrees nonetheless.
Mr. Compress notes how easy it was to convince the doctor. Kyudai admits that the plan was to always help but he wanted to see Tomura's development. He also admits that he cannot help until they get Gigantomachia to submit. Dabi interrupts saying he will not go back to fight Gigantomachia plus he has a good potential ally waiting. Kyudai interjects that Dabi can stay back to help him test the High-End Nomu Hood. Kyudai sends the remaining League of Villains members back to Gigantomachia at Tomura's request using Johnny.
During the following month and a half, Tomura and the rest of the League members fight almost constantly against Gigantomachia, having only a few hours of rest between combats. Keeping his word, Kyudai refuses to fully help the League until Gigantomachia submits. He only gives them a one-time meager allowance. During one of these breaks, they receive the call from Re-Destro, Grand Commander of the Meta Liberation Army. Re-Destro explains that the Army desires to destroy the status quo and allow people to use their Quirks freely, but the League's popularity is interfering with their plans, so they have kidnapped Giran. He explains that only the Army can be credited with the revolution that changes society, therefore the League of Villains must be eliminated to signal the Army revival. Re-Destro informs Tomura to go to Deika City in Aichi Prefecture within the next hour if he wants to get Giran back. He ends the conversation, giving Tomura two choices: 1.) stand against the Army and be destroyed or 2.) do nothing and be captured by the heroes when he gives their location.
Tomura decides to accept the challenge, saying he has a plan. He radios the doctor, who is surprise that the Liberation Army still exists. Mr. Compress thinks that Tomura is going to ask Kyudai to send a High-End Nomu, but the doctor clarifies that is not possible because they are not ready for testing and he cannot do much in regards to producing more Nomu without All For One's help. Tomura comments he did not want to rely on the Nomu, his plan is to kill two birds with one stone: use Gigantomachia against the Army. Once the Meta Liberation Army is decimated by Gigantomachia's rampage, he plans to attack Gigantomachia, hoping the Army weakened him enough to finally take him down.
The doctor yells how underhanded Tomura is being and wonders if Re-Destro was bluffing. Tomura replies, "Then the fool dies. Plain and simple." at the doctor's thought. They still have over two hours until Machia wakes up, and Tomura asks the Doctor to warp the entire League of Villains to Aichi. Once in Deika city, they are attacked by members of the Liberation Army.
Later on, members of the League endure almost an hour of battling the Meta Liberation Army and cause a large number of casualties to the opposing side, but members of the League begin to show weariness by the consistent battles and increasingly powerful enemies. Overhearing everything from his lab, Kyudai decides to help by waking Gigantomachia prematurely and ordering him to the League's location. Doing so causes, Gigantomachia to erupt from under a wooden mound.
After the fight with the meta liberation army and the merge with the league of villains, Tomura contacts the doctor. Kyudai is pleased with the progress such as Tomura regaining his memories, taming Gigantomachia, and comments on the reinforcement of the Paranormal Liberation Front and asks Tomura to do a little favor.
While the Paranormal Liberation Front prepares for when the time comes to attack, Kyudai prepares to perform an operation in Shigaraki to grant him even more power. Given that he is already very powerful, Kyudai asks Shigaraki why he wants even more power. Shigaraki gives you two reasons: first, because he had promised him more power if he met his requirements. And secondly, because he wants to use everything he has at his disposal to obliterate the drags All Might left behind.
Kyudai likes Tomura's proclamations and explains the situation. Thanks to the operation he will perform on it, he will obtain suitable body to control a power much greater than that of All For One, to the point he can even obtain the One For All. However, Kyudai also assures Shigaraki that the medical process will last four months, and he will endure four months of hellish agony.
With the situation clarified, Kyudai begins to operate in Tomura.
A month has already passed, and Dr. Kyudai is excited at how well his operation on Tomura Shigaraki is going; in fact, it seems to be going even better than he planned. Kyudai is impressed with Tomura and cheering him on from the sidelines while contemplating how, in the operating room, Tomura goes through a painful and gruesome process to obtain more power.
In late March, on the day that heroes vanished from the city, Dr. Kyudai is seen walking through a hospital. He greets a nearby nurse, who remarks that it's a rare sight to see him. Kyudai is in a pleasant mood, whistling while he thinks about the progress Tomura has made. He remarks that Tomura will be complete in under a month and that he can't wait. However, he's interrupted by Endeavor, who knows the truth about Kyudai and his relationship with All for One, causing the doctor to scream in terror.
Kyudai attempts to flee, but Aizawa grabs him with his capture weapon, then activates his quirk. Kyudai rapidly begins to age, revealing that he is not Quirkless, but has a longevity quirk similar to All for One. Naomasa deduces that Kyudai managed to artificially create quirks, replicating the rare regeneration quirk for the Nomus and offering his power to All for One. Present Mic grabs Kyudai by the collar and demands to know why he's using his power for evil. Kyudai demands the heroes to let him go, smiling as he waits for reinforcements to arrive.
Suddenly, several Nomu burst out of the floor. Kyudai's body begins to melt, and he reveals that he's a clone made by Twice. The real Kyudai is still in his workshop, preoccupied with his "masterpiece". Even so, he begins to panic at the fact the heroes discovered his laboratory underneath the hospital, revealing the countless number of quirks he's replicated throughout the years as well as the High-End Nomu he's still developing. He laments the choice but ultimately orders John to warp him and Shigaraki. However, Mirko bursts into the laboratory, incapacitating John before he can warp them and causing the doctor to scream in terror once again.
Kyudai watches on in horror as his laboratory starts crumbling apart thanks to Mirko sending multiple pieces of metal flying straight at his multiple test tubes and replicated Quirk jars. This also releases his incomplete High-End Nomus in the process. Mirko attempts to subdue the Doctor but the latter tells the Pro Hero that he is indeed the real deal. However, one of his Nomu "Mocha" intervenes by using Twice's Quirk in an attempt to create another Kyudai Double. Mirko manages to destroy Mocha before it does any harm and scrapes a bit of Kyudai's clothing. Having no choice but to flee, Kyudai reluctantly activates the remaining High-Ends to hold off Mirko and the other active Pro Heroes as he retreats to his workshop to complete Tomura's final upgrades.