Maka, Soul, Black Star and Tsubaki are sent to the grave yard for remedial lessons since they have yet to capture any souls and instead must capture a 3 star Meister Sid. Now that the group have captured Sid, they must find the evil that has turned him into a Zombie in the first place. But these lessons might be too hard for them to handle as the person who turned Sid into a Zombie in the first place is none other than Dr. Stein who is one of the top Scythe Meister to come out of the academy.
Once they find Dr. Stein, he lets them know that he turned Sid into a zombie for one reason, a simple reason, for his own experiment, nothing more. But Dr. Steins powers seem to be too much for the team to handle, his inner soul is 100 times larger then the team put together, AND he can change his wave lengths to match their own, AND he can focus his wave length with out a Scythe Weapon, AND he can use any weapon of his choosing because his soul is flexible, and he does this all out of his rolling desk chair.
Even Maka’s father, a Death Scythe is completely afraid of Dr. Stein and his power. The team never had a chance from the start.