Maka and friends arrive at the DWMA commemoration party. During the party, she sees Soul alone outside and tries to talk to Soul about any of his problems, with little effect. Annoyed that Soul had told Medusa of his dreams and not her, Maka tries to change the mood and asks Soul to dance with her. Soul declines, and when Spirit arrives, asking his daughter to dance with him, Soul persuades her to do so, much to her dismay. However, Maka leaves some food behind from the buffet for Soul.The party is interrupted when Medusa and her group begin to trap everyone in order for them to awake the Kishin. To prevent Medusa's group from awakening the Kishin, Asura, Sid is able to send Maka, Soul, Black Star, Tsubaki, Death the Kid, Liz, Patti, Stein and Spirit, underground to defend the school. Once underground, Stein tells them of how Medusa is plannning to reawake the Kishin that is sealed beneath Shibusen, and offers everyone a chance to back out of the upcoming battle. Along with everyone else, Maka declines and prepares herself, changing from her dress to her usual uniform, donning her trench coat.
They soon encounter Medusa. Black Star and Death the Kid, with their partners, run past Medusa. Maka also does so, by taking a risky path right through the blind spot of Medusa's attacks. She manages to pass through, and Stein stays behind with Spirit to battle Medusa.
Maka and Soul soon catch up with Black Star and Tsubaki, who are about to battle Crona. Although Stein had told Black Star and Tsubaki to fight Crona, Maka disobeys orders and tells Black Star to go on as she will fight Crona to avenge Soul. She expresses more confidence in the battle, and manages to aggravate Crona, and tells Ragnarok after he insults her that she is pleased that he is now treating her as an enemy rather than a meal. However, Crona still proves to be more pwoerful than her, countering her Witch Hunt with Screech Alpha. After seeing Crona gain the upper hand in their fight, Maka overhears Soul and Little Ogre and meets with Soul in the Black Room. Soul, shocked, thinks she is only a mere illusion that Little Ogre had created, but a Maka Chop from her shows him that she is real, and that they can converse to each other because their souls are in Resonance. The two dance together in the Black Room, and Maka tells him that she had heard Little Ogre after the Black Blood had temporarily infected her during the fight against Free, and urges him to accept his bargain for power when it appears to be their only chance of victory during their second battle against Crona. She tells him that she might gain more understanding of Crona's Soul Wavelength if she falls into the same sort of madness as him/her.
Soul appears reluctant, but he finally agrees, promising Maka that he will bring her back no matter how deep she sinks into madness. During this battle, the Black Blood causes Maka to fall into a crazed state of delirium, while Soul Eater holds on to both of their sanities, drowning in the darkness he refers to as madness. Because of the Black Blood hardening within her body, she is able to gain an immunity against slash and crush attacks and also acquirs superior strength, quickly overpowering Crona. While in this state, Maka is not only quite crazy but also quite silly, as her movements, behaviour, and her fighting style change drastically, and she resembles a state of inebriation. Her drastic behavior is clearly indicated by her swaying, constant giggling, and attempt to devour Crona's head. The true Maka is embarrassed by her actions, but Soul reassures her that her current state is no different as to how she usually acts. Soul tells her to quickly find Crona's soul. After passing by her own soul and her partner's soul, she sees Crona's soul. Whilst her physical self is crazily attacking him/her, her mental self manages to see into Crona's soul.
Later in their fight, she begins to understand Crona's soul and realizes that Crona has always lacked any sort of close relationship with anyone, not even with his/her mother, Medusa. As Soul manages to pull her out of the madness, Maka puts Soul aside, much to his surprise, walks calmly through Crona's Bloody Needle attacks (getting stabbed a few times in the process, although the Black Blood still manages to protect her) and embraces Crona, subduing him/her, stopping his/her rampage. Their fight ends with Maka asking to become Crona's friend. Crona starts to cry and decides to help Maka. Ragnarok, however, is displeased, and attacks Maka, which Soul and Crona try to prevent. Maka and Soul leave him/her behind to deal with the furious Ragnarok and help Black Star and the others stop the release of the Kishin.
On the way, Soul is concerned for Maka's wounds she had recieved, but Maka realizes that the Black Blood had healed them. However, she sees that her Black Blood is no longer in her body, and wonders why. However, she has no time to think as she senses Asura being released. She rushes to stop Asura. Despite her effort Asura is still released, but Maka still tries to stop him, grabbing one of his skin scarves and using Soul to try and slow him down. However, when Asura emerges above Death City, some falling debris hits her and she is left falling towards Death City. Luckily, Soul cushions the blow, probably saving her life. Maka still briefly tries to go after Asura, but loses consciousness. After Asura escapes, Soul carries her through the ruined Death City.
