Dr. Franken Stein is the most powerful meister to ever graduate from the DWMA. He is such a strong fighter that he could take down Black Star while still being seated in his chair. Stein is based on the central characters from Mary Shelley's novel Frankenstein, an amalgamation of the mad scientist and Frankenstein's monster itself. He has a bolt going through his head (which he turns to focus his mind) and stitch marks all over his body and clothes. Stitch marks are a recurring feature in everything Stein owns (including his house and furniture). Dr. Stein took up a teaching job at DWMA at the beginning of the series.
Stein is not entirely sane and constantly has to suppress the urge to dissect everything he sees. During the five years he was Death Scythe's partner, Stein secretly operated on him while Death Scythe was asleep. Once as part of a lesson Stein tried to have his class dissect an endangered animal claiming that it would be bad if he did not find out anything about it before it became extinct.
Stein's understanding of soul wavelengths gives him a huge advantage in battle since he can change his own wavelength to match that of his opponent, thereby disrupting the soul wavelength of the opposing meister and weapon. Stein can use this ability thanks to his high spiritual flexibility and by observing his opponent beforehand. He is a genius at utilizing his soul wavelength: even when unarmed he can channel it through his body and release it as a powerful current, create soul based shields or immobilize an opponent. While wielding Death Scythe, Stein is able to use the Witch-Hunt Slash for both long-range or close-range combat.
As the Kishin begins to revive, Stein notices that his own insanity is getting worse, and that he could very well lose control of his actions. Shinigami realises this as well, and has Death Scythe watch Stein closely. As Marie Mjölnir's soul wavelength is supposed to have a calming effect on the soul, she is assigned as Stein's new weapon. Stein's insanity grows yet worse when Medusa manipulates Crona into infecting Marie with one of her own snakes to speed up the effect of Stein's mania. Stein slowly but surely begins to lose the fight against his insanity. In the anime this culminates in him running away from the DWMA and unwittingly teaming up with Medusa. In the manga however Stein is implicated with the murder of a fellow DWMA colleague. Although he is warranted for arrest, Death Scythe, Kniges and Sid believe that Stein is innocent and allow him to escape with Marie to find the real culprit. Both Stein and Marie meet up with the real culprit, Justin and confront him.