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Doctor Franken Stein (フランケン・シュタイン, Furanken Shutain) is the man that changes Sid into a zombie. He is based on the central characters from Mary Shelley's novel Frankenstein, an amalgamation of the mad scientist and Frankenstein's monster itself. He was the most powerful meister to ever graduate from Shibusen.

Being a man of science, Dr. Stein sees everything in the world, including himself, as an experiment or specimen. This is the personality that he had as a child, as he often wanted to dissect the people around him. He was often stopped by Spirit. This personality trait made all those around him afraid of him. This strange hobby of wanting to dissect anything he thinks is interesting was still present, even when Stein became an adult, and once as part of a lesson, tried to have his class dissect an endangered animal, claiming that it would be bad if he did not find out anything from it before it became extinct. Stitching across his face suggests that he had worked on himself at one point.

He also exhibits a sadistic and intimidating personality. During his battle against Maka and Black Star, he would grab Maka by one of her ponytails, lift her shirt up and marks on her body, to signify where he would put the knife through, and thinks where he whether he should turn her skin into sandpaper. When Black Star tried to attack him, he countered by knocking Black Star out in a seemingly painful and bloody manner that made it seem as though he was killed. His smiles are normally filled with sadistic and dark intentions.

Stein seems to have dormant insanity. He has even admitted that he is especially sensitive to it. Medusa even stated that he is prone to insanity and a simple push was enough to drive it to surface. Stein ultimately did go insane and struggled to maintain it. He even quit smoking as a way convince himself. When struggling to maintain his madness, his personality was shown to make a drastic change, especially from his naturally curious personality to someone who did not care at all for the ongoing investigation at that time. He would soon lock himself up in his house when he was suspected and was even unsure of himself on whether he actually did kill BJ, even after he had locked himself up.

He has a habit of smoking to the point that he is seen with one in nearly all his appearances outside of battle. He even smokes a specific brand of cigarette. The lady he buys them from imports them just for him. His propensity to smoke was used against him when Spirit and the rest suspected that he killed BJ, purely due to the fact that a cigarette brand he smokes was at the crime scene and he smelled of cigarette. When he went insane, he stopped smoking because he believed he would not be able to stand his madness if he could not stand against his habit.

Emotionally, Nygus has described him as always alone and that he has no love in him. He has admitted that he can't understand Spirit's reaction to Maka asking him to go out shopping. This shows he can't feel deep emotions other than the need to dissect whatever interests or irritates him. This tendency likely seems to be more destructive or psychotic, which explains his dormant madness. He has shown to be a bit morally bankrupt, at least back in his youth. In Sid's flashback, he questioned Sid's decision to adopt Black Star, who was a baby. This suggests that if it were Stein's decision, he would have left Black Star. His immorality is supported further by his repeated experiments on Spirit back when they were kids.

Despite this cruel and twisted personality, Stein does have a kind and compassionate side that worries for the people around him and he feels the need to protect them. He also exhibits a rather paternal demeanor towards his students. He also expressed deep disgust and moral outrage towards Medusa for regarding Crona as nothing but refuse and research material. It is never stated when this other personality arose, it could be assumed it happened after Spirit left him and went with Kami.