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Long ago, much of Franken Stein's own violent tendencies and initial selfish disposition surfaced in his childhood, having been analyzed and examined by various doctors to determine the cause of his personality. Although they speculated that he must of suffered some traumatic event, the doctors couldn't conclude deduce the reason and Franken Stein himself only saw their attempt as inane. At one point during Kindergarten, Stein would watch kids his age play together like the teacher told them, an act which sickened him. He also made an issue out of the children focusing on taking notes and listening to instructions given to them from the teacher; this made him feel as if he would lose control over himself.
Time in the DWMA
After joining the DWMA, he was set as Spirit Albarn's partner. He would abuse his position and even beat up people not on Shinigami's List. This caused Spirit to get involved at one point and do his best to stop him. As he would adhere Spirit's word, he them claimed he wish to be born in a world without god. However, when Spirit asked him If he was serious, he dismissed that notion, stating that such a world would be "sick".
During his time within the DWMA, Franken Stein would secretly experiment on Spirit's body for years. He also dated Marie Mjolnir but later broke up with her. He was also participated in the purging of the Star Clan. Seeing Sid Barrett thinking about taking a young baby, he questioned his decision on what to do with it. However, this earned him a chastising from his weapon partner and would understand the reason his partner feels a certain way was due to his own daughter being born soon.
Soul Eater NOT!
After Shaula Gorgon ordered Eternal Feather to kill herself, it is Stein who performs surgery on the latter, thus he manages to save her. He also plays various jokes on Tsugumi, Meme, and Anya by making her seem like she was transformed into a Zombie along with having a screw on her head like himself.
Stein's first appears when Maka, Soul, Black☆Star and Tsubaki appear in front of his home, on orders to capture his soul by Death. Stein provoked this order by transforming Sid into a Zombie. He comes outside, after tripping and falling off of his chair, and takes note of the Shibusen kids. Stein, using his advanced Soul Perception abilities, looks at Maka's and Soul's wavelength, and proceeds to tell them that, Maka's soul, who is serious and a hard worker, does not stabilize well with Soul's sarcastic and twisted soul.
Black☆Star then interrupts their conversation, stating how boring it is, and recommends them to start one strictly about himself. Stein then views Black☆Star's soul and states it is "a terribly self-absorbed soul." With that said Black☆Star proceeds to kick Stein, only to be blocked and quickly given a powerful punch. He then notices Black☆Star's partner, Tsubaki, and notes that her soul is very co-operative and has plenty of room to accept people. After that, Stein states he will start the session.
Despite the efforts of both Black☆Star and Maka, Stein easily dodges and counters all of their attacks, all the while still remaining seated on his chair. Stein then displays his powers by striking Maka's weapon and disrupting their wavelength. Stein then grabs Maka and threatens to dissect her, only to be interrupted by Black☆Star, who manages to connect his Big Wave. Unfortunately, it is ineffective, as Stein managed to match his wavelength with Black☆Star, nullifying the attack. He then attacks Black☆Star, releasing a Soul Menace upon Black☆Star, apparently killing him.
Soul, angered by this, proceeds to attack Stein, only to be stopped by Maka, who is daunted after seeing the size of Stein's soul, and concedes that the difference between their strength is insurmountable. Soul, however, refuses to give up and, through a small pep talk, manages to rekindle Maka's fighting spirit. Together, they conduct a resonance between their wavelengths and perform Witch-Hunt. Stein is not daunted by this and takes the attack, barehanded. With some sign of actual effort, he manages to break it, knocking Maka away. Before he can put his hands on the fallen Maka, Soul appears and guards her. Stein, impressed, pats Soul on the head and gives him a passing grade for being willing to protect his Meister with his own body. He reveals that this was all a plan orchestrated by Death and, as it turns out, Black☆Star was not killed, but merely knocked unconscious.
The New Student and Soul Observation
As the new teacher, Stein decides to take a different route in his teaching by dissecting a natural world souvenir animal. He is, however, interrupted when he is forced to supervise the battle of Death the Kid against Soul and Black☆Star. He then preps Maka on the stability of Kid and his two weapons, Pattyand Liz; noting that they respect and admire each other.
Demon Sword Ragnarok
After Maka and Soul initially encountered both Crona and Ragnarok, a battle ensued between the two pairs. The battle begins to go in Crona's favor and Maka looks to be in serious trouble. However, before the final blow is dealt on Maka, Spirit and Stein appears just in time to save Maka from Crona. With Maka saved, Spirit transforms into his weapon form, wielded by Stein, and prepares to do battle with Crona. During this battle, Stein deftly wields Spirit, blocking all of Crona's attempts to damage him and retaliating with his own devastating Soul Purge. After prolonged abuse by Stein, Crona is eventually defeated. It is then that Medusa, Crona's mother, appears. After scolding the unconscious Crona for failing, she proceeds to attack Stein with her Vector Arrow. Performing a Soul Resonance, Stein uses Witch-Hunt to deflect the arrows. After this failed attempt, Medusa takes Crona and makes her escape.
Back in the infirmary, Stein confronts Maka and tells her that the procedure on Soul was a success. This cheers Maka up. Though, when confronted by Spirit, Stein reveals that the surgery was fine, but the Black Blood of Ragnarok has invaded Soul's body, and is unsure if he will be okay.
Post Kishin's Revival
After he tries to kill Medusa, and the Kishin revives, Stein mentions that the kishin's wavelength brings out the Madness in everyone. He himself notices that since his own madness is extremely large already, this effect could come to his madness possessing him. Death also sees this, and has Death Scythe watch Stein closely. Marie Mjolnir is assigned to be Stein's new partner as her soul wavelength is supposed to have a calming effect on the madness. After Medusa takes the form of a little girl, she instructs Crona to slip a snake into Marie's coffee which increases Stein's madness wavelength, and at one time renders him unable to fight. Even without this magic, Stein is slowly losing the fight against his madness, and he knows it. Stein is implicated as the murderer of a fellow Shibusen colleague, Joe Buttataki, but Death Scythe, Mira Naigus and Sid believe Stein is innocent and allow him to escape Shibusen with Marie to find the real culprit.
Operation: Capture Baba Yaga's Castle
During the conclusion of the infiltration of Baba Yaga's castle, it is stated by Medusa that although she was present at B.J.'s murder she did not kill him and that Stein should be close to catching the culprit about now.
Tying Things Up, and New Beginnings
Stein only reappears after discovering the truth behind Joe's death, revealing that it was in fact Justin Law, a fellow death scythe, who had committed the murder. It is then explained that his and Marie's long absence was due largely to the difficulty in discovering Justin's current location. Marie firstly questions Justin about his reason for killing B.J., only receiving simply the reply that his "Soul Perception ability was too dangerous...the Kishin-sama was unable to rest easily". After hearing this and deducing that his next target was Maka, she charges towards him and hits him in the chest. It appears her attack has little effect but after extending part of her weapon from her fist, Justin is sent flying yet he still manages to recover in mid-air to land safely. Observing this ineffective result, Stein questions her on whether or not she was now even, before asking her to assume her weapon form so both her and Stein could go on the offensive. The resulting speed, enhanced by Marie's abilities, easily overwhelms Justin, who couldn't even re-act to their attacks, forcing him to retreat using an artifact. This leaves Marie and Stein in the desert outskirts of Death City, with nothing but the coffin Justin left behind.
When Stein and Marie eventually return to the Shibusen, both they and Spirit are brought before Death. They all proceed to apologize for their individual transgressions, with Stein focusing upon how his running away was in flagrant defiance of the regulations. Death appears unfazed and simply asks for all of them to say sorry. Stein then reveals that he has uncovered proof of his innocence and of the true culprit. Marie takes out a tape recorder and plays back what was supposed to be their previous conversation with Justin, unfortunately all that was recorded was 5 full minutes of his background music. Stein smiles and light halfheartedly comments upon the situation, before Spirit reveals that he had been conducting his own investigation, proving Justin as B.J.'s murderer. Stein replies by stating the information they had discovered, specifically concerning Justin's acquaintance with someone with magical connections.
Stein is seen again discussing with the members of "Spartoi" as to what it the group’s name means and why it was changed.
Tezca, Sid, Nygus, Marie, and Stein arrive at Noah's place. Tezca is killed as soon as he walked in, then Sid and Stein are attacked by one of many of Noah's 'worm' things. Later on, he is restrained by Noah, however seems to be freed as the Spartoi members jump out the book. He refers to himself as "fatally injured", however he appears in later chapters having recovered.
Stein killed one of the Clowns that snuck on board the ship before landing on the Moon. Stein's personality seems to confuse his comrades. He remarked Marie and Spirit that he came to the Moon because he was allowed to "dissect" the enemies. When he was fighting, Spirit is worried and compared him to a Kishin. Stein fights against Justin and continuously dodges every single attack. He then managed to hit him directly with a powerful Soul Menace with Marie's help of channeling a massive amount of Stein's wavelength through her. Stein's mind is still normal even when he is deeply influenced by Madness.
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