Maka and Soul, resuming their soul hunting, defeat and acquire the soul of the Evil human, Rasputin. The morning after, Maka walks in Soul's room to find him with Blair, who had snuck up on him. Misunderstanding the situation, Maka kicks Soul out of the window in fury. Later, at school, Soul tells her of a rumour that had been going around recently. Their homeroom teacher, Sid Barett had been missing and rumors had gone around that he might be a zombie attacking students. Maka is frightened by Soul Eater's retelling of the stories but tries to write them off as meaningless rumors. Much to Maka's dismay, her father becomes a temporary replacement for their homeroom teacher. However, the two are sent to the Death Room to see Shinigami. On the way, they meet Black Star and Tsubaki, who had also being called to the Death Room.Shinigami, upon meeting them, informs them that they all must take extra lessons. Maka is shocked by this, thinking that extra lessons are only for idiots, however, she is soon demoralized when she is told that she has acquired a low number of souls as of now. Shinigami informs them to go after Sid, who had indeed been turned into a zombie, and find who had turned him into one. If they do not succeed, all four of them will be expelled.
The four decide to go to Sid's grave in Hook Cemetery to start their investigation. Maka is still too depressed to care because of her having to take extra lessons. However, she soon readies herself as Sid attacks them. A battle soon ensues between the students and teacher. This fight is the first time in which Maka uses Soul Resonance and her Witch Hunt attack, resulting in a near-death experience for Black Star after she missteps and incorrectly aims. Maka and Soul argue as to who botched up the Resonance. Black Star ends up catching Sid using Tsubaki in Weapon form (unintentionally catching Maka and Soul too, much to their chagrin). In trying to get Sid to tell them who had made him into a zombie, Black Star flips Tsubaki's skirt, revealing her underwear. Sid relents and says that is was Stein who had made him into a zombie, but refuses to tell them where he is. Soul, refusing to give up, flips Maka's skirt also, covering his eyes. To Maka's annoyance, Sid shows no reaction towards her. She ends up giving Black Star, Sid and Soul a Maka Chop and Sid ends up telling them where Stein is.
The four then proceed to Stein's lab to encounter and deal with the source of the problem. After a rather bemusing introduction, it is concluded that the only way to resolve the issues is to defeat Stein. It is only when the fight begins that Stein reveals just why he had earned his reputation as a strong fighter, by easily taking on the team single handed, intimidating Maka and apparently 'killing' Black Star. Maka rightfully begins to fear Stein and this is only furthered when she observes his far stronger soul, using Soul Perception for the first time. It appears that she is frozen by her fear, but Soul manages to encourage her to fight him, saying that just because she had seen his soul, she has not seen the future. The two attack again and successfully Resonate and connect their Witch Hunt. Unfortunately Stein is still able to overpower the attack, leaving Maka barely conscious on the ground. Before Stein can grab her however, Soul appears and crouches over Maka, telling him that he will not let him hurt his Meister. Stein, pleased by Soul's bravery, gives him a pass point, and Stein reveals that the lesson has now ended. Everyone finds out that Black Star is actually alive and that this was all a part of the extra lesson, much to Maka's despair. From this point onwards Stein becomes Maka's teacher. Maka, horrified, actually starts to want her father to be her teacher instead.
