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Stein is a respected instructor in the the DWMA; his students are said to love him as a teacher, despite his disturbing tendency to favor doing lessons on dissections. He's also known as the strongest meister to have graduated from the DWMA. However, due to his sensitivity to madness, he often can be called to be questioned on his sanity. Despite this, however, many of his friends like Spirit, Marie, Sid, and even Death have shown faith in Stein.
Marie is assigned to be Stein's new weapon partner as her soul wavelength is supposed to have a calming effect on his madness. Stein was also apparently Marie's first love when they were still attending the the DWMA. However these strong feelings seemed to only be one-sided by Marie. It is possible that Marie never openly expressed her romantic feelings towards Stein in the past, and tries to hide them, as Stein appears to be completely unaware that he was Marie's first love. As a result of Marie's restraint, Stein only sees her as somewhat of a best friend. It is unknown if Stein would view her more passionately if she were to express her feelings towards him. It is also kept in mind that Stein has said that he is incapable of understanding love; however, this statement is slightly contradicted by his relationship with Medusa. Although, due to Stein's madness starting at a very young age, feelings such as love may not have developed at the normal age. It would be reasonable to assume that Stein may learn of love if it was given to him. Any possible romantic aspects of Stein and Marie are not explored much in either the anime or manga, though Stein is seen as being very, almost fiercely protective of Marie. It should also be noted that many of the people around the two insinuate romantic connection, such as when Spirit asks if the two were back from their little 'honeymoon' after returning from the search for Justin. By the time the Kishin was defeated, it is assumed that the two have started a romantic relationship, as Marie is now carrying Stein's child.
Spirit and Stein have a complicated relationship: they have known each other as classmates since they were young students at the Death Weapon Meister Academy, they resonate well due to Spirit's adjustable wavelength and Stein's skill, but Stein's trickster personality, Spirit's emotionality, and the threat of Stein's falling into madness to slice up Spirit compromises their partnership.
Stein was Spirit's first meister. While working with Spirit, Stein would often conduct experiments on him during his sleep. They still retain their strong friendship from back when they were partners, despite the fact that Spirit is still somewhat traumatized by Stein's past procedures. This friendship continued when Stein and Spirit observed the remains of the DWMA's battle against the Star Clan, where Sid Barrett found an infant as the clan's last survivor, Black☆Star.
Outside of battles, Stein often likes to tease Spirit about how often he would attempt to vivisect and experiment upon him, very amused with the reactions he is able to provoke from his former partner, which is not very surprising considering that Spirit constantly refers to Stein as being overly sadistic. This fact is clearly illustrated when Stein jokes that he switched Spirit's left and right middle toes with each other, causing Spirit to immediately remove his shoes to see if what Stein had claimed to have done was true. Stein frequently ridicules Spirit in a calm way, even going as far as calling Spirit an "idiot" on several occasions, just to set Spirit's fuse off and have him lash out at Stein.
However, Stein is shown to still have a soft side for Spirit, as he still refers to him as "Senpai", even though Stein is commonly displayed as the superior.
Despite how dangerous Stein has been and can be to him, Spirit remains dedicated to his former meister, willing to work with him to fulfill Death's orders, especially when those orders concern the safety of Stein's student and Spirit's daughter, Maka Albarn. Although initially terrified to find Stein back at the DWMA, Spirit puts aside his fear to join Stein in Italy to save Maka and her weapon Soul Eater from Crona and Medusa. Stein also expresses thankfulness that Spirit happened to be underneath the Academy before Free's Independent Cube trapped their colleagues during the Kishin's revival, saying he would need his partner in combat.
In his concern for Stein, Spirit tries to do what is best to help his former meister retain his sanity. When evidence pointed to Stein being the murderer of Joe Buttataki, Spirit was not convinced, refusing to arrest him. Instead, along with Sid Barrett and Mira Naigus, Spirit directed allow Stein to escape Death City with Marie Mjolnir to locate Joe's actual killer. Spirit's faith proved appropriate, as Stein and Marie, along with Azusa Yumi's separate investigation, were able to prove Justin Law was the killer. Spirit's concern for Stein's sanity also leads him to suggest Stein, at his age, have a family to resist madness—unaware that Marie is already pregnant with Stein's child, and despite Stein mocking Spirit, a divorced philandering parent, hardly a role model to recommend having a family to have a more orderly life. Nevertheless, Spirit joins with Kid in glee upon learning that Marie is expecting a child.
When Soul Eater fell under the sway of madness emanating from Crona's Black Blood spheres, Stein ordered Kim Diehl to fall back while he wielded Jacqueline. Jacqueline readily followed her teacher's instructions, and while Stein was able to wield her expertly, they were unable to prevent Soul's Death Scythe abilities under madness from cutting both of them. When Stein was able to hold onto both Maka and Kim in his arms to dodge Soul's attacks, Jacqueline complimented her teacher's skill at dodging these attacks with such heavy weight, offending Kim.
Stein seems to respect "Shinigami-sama" immensely, apologizing to him after "breaking regulation." He also accepts requests from Death, as when he requested Stein help some students on their Extra Lessons, which including a request to turn Sid Barrett into a zombie. He also fulfilled requests made on behalf of Death's own Death Weapon Meister Academy, despite his initial resistance to join the Academy as a teacher: before returning to the Academy, he fulfilled Sid's request to investigate what possessed Eternal Feather and Mira Naigus's request to produce an antidote to this agent.
Stein has so much respect for Death due to his own desire for "a system set up by a god without arrogance," suggesting he sees Death as without arrogance. In the anime Medusa mentions that Death will be one of the primary figures Stein's mind will use during his descent into madness, in an attempt to control himself from her spell.
Stein expressed some surprise when Sid recovered the infant survivor of the Star Clan, Black☆Star, but seems to have accepted Sid adopting the baby. During their youths, Stein and Sid had, likely on separated occasions, attempted to meet with the Holy Sword, Excalibur, and the two commiserate in front of Tsubaki Nakatsukasa about how miserable it was to deal with that annoying weapon.
After Stein left the DWMA, Sid frequently spoke with Stein, attempting to convince him to return to the Academy as an instructor. Such appeals seem not to convinced Stein, until after Sid's death when Death approached Sid himself to ask that the scientist investigate reports of a witch who was experimenting on a certain meister. How much Sid's death and his previous attempts to convince Stein to come to the Academy is unclear.
Stein is also one of Sid's trusted physicians. When Sid died, his corpse was brought to Tsugihagi Research Laboratory before being ostensibly buried in Hook Cemetery. It was likely during this time that Stein turned Sid into a zombie, per request of Death in order to test Maka and Black☆Star in a remedial lesson. While Stein could not return Sid back to normal, Sid does not seem to mind: while a significant change for Sid's life, he seems to maintain a friendship with Stein, bragging to their students how great life as a zombie is, although this performance was likely to play the villain in the remedial lesson that Sid and Stein organized for Maka and Black☆Star. Stein may also have been the person who reattached or replaced his arm after it was cut off by Noah's Magic Worm.
Sid and Stein worked closely in numerous missions, including the investigation into Medusa's revival of the Kishin, the rescue of Death the Kid from Noah, and the fight against Asura on the Moon. While Stein shows concern about Sid and Mira facing a suspected witch like Medusa, Sid assures his colleague that he understands the risks. When Death issued a warrant for the arrest of Stein on suspicion of killing Joe Buttataki, Sid's experiences with Stein as a colleague and friend convinced him that the scientist did not kill Joe. Therefore, Sid allowed Stein to depart with Marie Mjolnir to locate the real killer.
Stein appears to share a mutual disliking toward Azusa with Spirit. As the two simultaneously recognize her by her pet name, "Queen of Committee Chairmen," upon seeing her again in the halls of the the DWMA for the first time in years. Stein complains that Azusa never let him dismember a passerby in the past, however Spirit took Azusa's side whenever she did this. Interestingly, she seemed not to like him dissecting anything; she is seen to be about to tell on him when he was about to dissect a bird, perhaps publically, which may have been a leading factor in this disgust. Nevertheless, Azusa is the one who assisted Stein, indirectly, in exonerating him of the murder of Joe Buttataki, and they are both adamant about stopping the Kishin.
Although Stein and Joe both dated Marie, the two seem to have no ill will towards each other. Due to his concerns for Marie as Stein's most recent weapon, however, Joe does warn Marie that he is concerned about Stein's madness, and as an investigator he intends to observe Stein carefully in case he is the mole within the DWMA.
As one of Stein's colleagues at the DWMA, and as someone close to Marie, Stein takes on the mission to locate Joe's actual killer, as well as to clear his own name against accusations that he murdered Joe. Stein and Marie's investigation, coupled with evidence presented by Azusa Yumi, exonerates Stein and shows it was actually Justin Law that murdered Joe. To avenge Joe's death, Stein joins Marie to attack Justin, facing the defected Death Scythe repeatedly in combat, including on The Moon.
While initially goofy in his interactions with these students, Stein largely a serious instructor in the classroom and on the battlefield. While he writes trick questions in his classroom exams and will skip important lessons to instead conduct vivisectiosn and dissections on endangered species, Stein does take his work seriously to train Maka and Black☆Star as capable meisters for Soul and Tsubaki.
On orders from Death, Stein served as an imagined antagonist to Maka and Black☆Star as part of a remedial lesson. As Death and Sid Barrett, now a zombie, feigned that Stein was a threat to the DWMA, Stein played the role of a villain, bragging of his desire to vivisect and kill others for the sake of science. Although certainly crazed, Stein was in control for much of the fight, making sure not to kill the students as he fought them. Stein was so careful that he faked the death of Black☆Star with careful use of Soul Menace to only shock, rather than kill, the ninja. When Maka faced Stein with an improved Witch-Hunt attack, Stein was impressed to see how this student did, perhaps with some happiness based on his previous partnership with her father and despite his potential frustration that her mother revealed his mutilation of Spirit's body. Overall, Stein was both amused and impressed with the students: when Soul offered to sacrifice himself to save Maka, Stein concluded the lesson, confident the quartet had learned much from this seemingly dangerous encounter.
When teaching Maka, Stein can be firm, even strict, but he recognizes when to be more encouraging. Recognizing Maka's self-doubt following Soul's injuries before Crona, Stein tells her to consider what it is that she is lacking in quality to improve as a meister, either confident that she could determine the answer herself, or refusing to give her answers easily. Stein was impressed that Maka realized that what she was lacking was courage and offered to conduct a special lesson, even on a weekend, to help her and Soul improve their Soul Resonance and partnership. Therefore, Stein tends to let Maka come to decisions on her own, although he is not above chastising her when he determines she needs to be contradicted: when Maka asked Stein to remove Black☆Star from her chain resonance team, Stein refused, claiming it was Maka and not Black☆Star whose weaknesses in teamwork and even power were holding back her team. Upon seeing Maka overcome her frustrations with Black☆Star to work as teammates, Stein demonstrated his confidence in her by naming her leader of her three-meister team consisting of her, Black☆Star, and Kid.
While Stein was initially hostile, even perverted, upon meeting Maka, complimenting her on her smooth skin and lifting up her sweater and shirt, Maka seems to have developed a close mentee-mentor relationship with him: upon his return to the DWMA after investigating Joe Buttataki's murder, Maka rushed to hug Stein. Maka demonstrates considerable concern for Stein's safety against madness: she used her Anti-Demon Wavelength through a hug to mitigate the madness infection that Soul was causing him in Russia, and in the anime she joined Crona and Marie Mjolnir to fight against Medusa and rescue Stein from her madness infection.
Whereas Stein focuses on negotiating with Maka through lessons focused on talking, when contending with Black☆Star, Stein focuses on fighting. Understanding that Black☆Star learns physically and tends to set his goals far higher than may be advisable, Stein practices a hands-off approach to let Black☆Star learn through his mistakes, in the classroom and in combat. When offering Black☆Star a jar of Kyūkon Water, Stein ordered him to attempt putting in only one finger at a time—but seeing Black☆Star would not follow instructions, Stein offered a rather lenient response and allowed the ninja to proceed. While shocked that Black☆Star ended up drinking the water, and surviving, Stein determined that it is best to let Black☆Star proceed as he will. Therefore, their later training usually occurred outside of the classroom and in sparring matches, as Stein told Black☆Star to keep practicing to learn from his errors. It is likely for the best that Stein taught Black☆Star outside of the classroom, as many of their interactions depended on physical engagement: in their first battle, Stein shocked Black☆Star so badly that his classmates thought he had died, and when he caught Black☆Star stealing his Ultimate Written Exam from Tsugihagi Research Laboratory, Stein pummelled Black☆Star and allowed Sid Barrett to hang the student's barely conscious body in Class Crescent Moon as an example to any students considering cheating.
While his interactions with Tsubaki are limited, Stein is not above to putting the very polite student in her place as an example of his strictness: if he is willing to throw a scalpel at such a kind student as Tsubaki for speaking in class, Stein seems to think, then he is willing to do much worse to any students who are much worse students.
Even if Kid is Death's son, Stein is not above criticizing him and his students, as well as having more prurient desires. Upon seeing Kid duel Soul Eater and Black☆Star on Kid's first day of class, Stein is distracted by his desire to cut into Kid's pristine skin. Stein also does not play favorites with Kid, as when he and Sid failed him on the Ultimate Written Exam based on his inability to complete the test, let alone write his name atop it.
Stein also has used the Thompsons as an example of students who are insufficient for his initial Duel Arts lesson, although the insult only amused Liz and Patty, while Kid was embarrassed at the siblings' refusal to take that criticism seriously.
Yet Stein does show his confidence in Kid. As he claims to desire "a system set up by a god without arrogance", he likely sees Kid, like his father, as without arrogance. During the mission on the Moon, Stein encourages Kid to retreat back to Death City, as his role as the new Death requires that he negotiate with the witches, not only fight along his peers. Stein seems to admire Kid's willingness to fight with his adult allies and mentors, even as he gently guides Kid to pursue a political solution rather than only fight this war.
Following Shaula Gorgon's possession of Eternal Feather at the Death Bazaar, Stein takes an interest in Eternal Feather's recovery in order to determine a cure against Shaula's mind-control venom. Stein saves Eternal Feather's life against her possessed attempted suicide, then meets with her repeatedly for follow-up recovery. While fulfilling his obligations as a physician, Stein is not above lapsing into his perverted desires and interests in vivisection, thinking how much more "sexy" the teenage Eternal Feather would be as a zombie.
Eternal Feather credits Stein for saving her life, for which she is grateful. She seems to regard the physician as an amusing person, as the two share a similar sense of humor. For example, after Stein tricked Tsugumi, Anya, and Meme to think he had put a screw similar to his own through Eternal Feather's head, then had a the head of a robotic duplicate of Eternal Feather chase the trio, Eternal Feather herself borrowed the screw, the robotic head, and even a wind-up screw to twice trick the three NOT students to think she was indeed made into a robot and to allow the robotic head to chase after them. While Eternal Feather played these tricks to get into the trick-or-treat spirit of Halloween, it is possible Stein allowed her to do so for his own amusement, not only to help her.
Tsugumi is grateful to Stein for saving not only Eternal Feather's life, but for providing the only vial of antidote to Shaula Gorgon's Venom despite Mira Naigus's orders not to. However, when dealing with Tsugumi and her meisters Anya and Meme, Stein is prone to prank the trio for his own amusement. When first meeting the three students, Stein created a robotic duplicate of Eternal Feather to pretend that he fashioned her into a disembodied, living head, then into a person with a screw through her head, seemingly only to have fun at the students' fear. While Anya tends to react with more hostility to Stein's pranks, threatening to attack him, Meme seems passive while Tsugumi is more bemused than infuriated.
In the anime, Stein assisted Meme with her recovery from injuries and mind possession sustained during her time working, against her will, for Shaula Gorgon.
Medusa has consistently had strong feelings towards Stein, mainly because of their common interest in science and doing things they aren't supposed to. Medusa even went as far as to infect Marie with her snake, in order to drive Stein into madness, in the hopes that it would eventually lead him to her. The only sign of affection Stein returned was during the anniversary party at the the DWMA where they almost shared a kiss, Stein noticeably remains perfectly still, until the kiss is stopped when Sid came shouting from the other side of the room. This is the end of any romantic insinuation between the two, as, later in the arc, Medusa tells Stein that she loves him and he promptly stabs her with Spirit. It often appears more that Medusa sees Stein as a toy to be played with; seeing him as a rather silly man but her sister Arachne revealed that Medusa does in fact have a crush on Stein.
Stein and Justin seem to serve as foils to each other, Stein at one point claiming he would be fearful should he "commit heresy against Shinigami-sama," similar to Justin's initial presentation as a devoted follower of Death. As well, upon meeting with Justin during the Death Scythes' meeting with Death after Asura's escape, Stein remarks that Justin is someone who will not fall into madness as he would, contrasting the two fighters. Despite acknowledging this difference between them, Stein seems to make this remark with no malice towards Justin.
Justin, however, serves as a major antagonist to both Stein and Marie Mjolnir, having killed Marie's former boyfriend Joe Buttataki and leaving Stein as a suspect. At the scene of Joe's murder is a carton of cigarettes, the same imported kind that in all of Death City only Stein orders. Once Stein and Marie find Justin and accuse him of killing Joe, and intending to kill other meisters with strong Soul Perception such as Maka Albarn, Justin begins to act hostilely to the two. Even as Justin wears a smile during his initial fights with Justin and Marie, he does not resist mocking the two, including some misogynistic remarks against Marie.
Stein and Marie are the ones who kill Justin during their final battle on The Moon in the DWMA's mission to contain Asura. Even as Justin mocks the two because he thinks that they will never defeat Asura, he cannot help but obsess with the question; why do Stein and Marie still persist in this battle despite such hopelessness? Why is Stein, someone who seems to be so much a nonconformist, siding with the DWMA, the very representation of Order itself? Justin accuses Death of sending his followers to kill anyone who does not share his view, and Justin cannot understand why Death's order is so precious. As Stein renews his Soul Resonance with Marie, he answers that Death actually does not demand absolute conformity to his whims. Justin does not move as Stein approaches to kill him, and he is still not convinced by Stein's explanation: once Death eliminates all such targeted heretics, where will Stein direct that Madness then? As Justin's severed head evaporates, he still speaks, with a warning to Stein and Marie: "Have no fear...Your time will come. Order will crumble to dust." 
- ↑ Volume 2: Chapter 2's lesson is "We'll be dissecting frogs today!" Maka also claims in Chapter 3 that they have done 'nothing but dissections' since he took over her class. (Yen Press translation)
- ↑ He also implies that they have taken apart frogs and mice, in Chapter 3. "He-he...what you'll be taking apart today [the endangered species of bird] isn't the usual frog or mouse. ♪"
- ↑ Soul Eater, Chapter 1, Volume 1, Yen Press translation. "That's right. Stein-kun was Death Scythe-kun's first partner. He was the strongest meister to ever graduate from this school." (Death)
- ↑ Soul Eater Manga: Chapter 113
- ↑ Soul Eater Volume 2, Chapter 2. "While I was asleep... he... he... ...he would do experiments on me!! And he did them for five whole years!" (Spirit, Yen Press translation)
- ↑ Examples of this include: "Senpai? You can block that Demon Sword, right?" in Volume 2, Chapter 5, (Yen Press translation).
- ↑ Soul Eater Manga: Chapter 81
- ↑ Soul Eater Chapter 2
- ↑ 9.0 9.1 9.2 Soul Eater Chapter 21
- ↑ Volume 7, Chapter 23, Yen Press translation. "Every time I tried to take apart some random innocent passerby, she always ran and tattled on me."(Stein) "Actually, I'm with her on that one." (Spirit)
- ↑ Volume 7, Chapter 23 depicts a younger Stein about to take apart a bird with Azusa pushing up her glasses menacingly, suggesting that she is about to tell on him.
- ↑ Soul Eater Chapter 101: Volume 23, Yen Press English translation, page 121
- ↑ On the last page of Chapter 12, it says on the exam results that Kid and Black☆Star were 'left out of consideration' (Yen Press translation) with 0 points. They also presumably had to take a makeup exam because they scored lower than Soul.
- ↑ Volume 22: Chapters 4 and 5 (Yen Press translation)