Soul Eater Maka Albarn Part in the Story-Seiken

Maka is next to Soul when he wakes up from a terrible dream, and tries to comfort him. Later on, Maka asks if she can do anything for Soul; Soul replies with a no. Maka is noticeably saddened by this. Soul tries to cheer her up by saying it is his fault that he is in this condition. This only saddens her more as he makes her leave. Outside of Soul's room, Maka's father asks her to come up to the roof with him.
Up on the roof, Spirit tries to cheer up Maka, which proves fruitless. Maka asks Spirit what he thinks of her mother. When Spirit replies that he loves her, Maka asks why he cheated on her all the time. Spirit tries to run away by asking her if she wants to head back. Maka says they just got there.
Later on, Maka asks Spirit about the Kishin. He then explains the origins of the first one, Asura.
After Black Star and Kid's meeting with Excalibur, Maka, along with Soul who had recovered, shows them a large bouquet of flowers Excalibur had left for them in their classroom, and a message to them that he will be waiting for them.

Soul Eater Maka Albarn Part in the Story-Demon Sword Ragnarok

Maka and Soul go on a mission in Italy. After a run-in with the Materazzi, the two successfully defeat and acquire the soul of Sonson J. After a brief conversation with Soul, Maka detects an unusual soul within a church and decides to investigate, believing it to be another Meister and Weapon. She detects the souls of the Materazzi, but to her shock, all of their souls disappear in an instant, as if they have been devoured. The two ride to the church on Soul's motorbike, and enter the building.
The two do encounter a Meister and Weapon: Crona and his/her Weapon partner that shares a symbiotic relationship with him/her, Ragnarok. It is revealed that they had killed all the people present, and they then proceed to attack Maka and Soul. Maka and Soul put up a good fight but are overpowered due to the abilities of Crona's Black Blood. Maka worries about Soul as she realizes that Crona can hurt him, even in Weapon form. However, Soul tells her to keep using him, as he is prepared to die for his Meister. However, Maka is cornered, and is reluctant to use Soul to block one of Crona's blows. Soul transforms into human form and shields her from the blow, acquiring a large scar across his chest. Maka, deeply upset over Soul's sacrifice, refuses to leave him behind as he tells her to escape before losing consciousness. However, the two are saved by Spirit and Stein. Stein assures that he will do what he can to save Soul before fighting Crona and Ragnarok. Maka watches the two battle and eventually they are successful in defeating Crona and Ragnarok, but the sudden appearance of a Witch, Medusa, allows Crona to escape.
Maka, deeply worried about Soul, waits for Stein to finish operating on him outside the dispensary back at Shibusen. When Stein allows her to see him, she tearfully stands at his bedside, promising Soul to become stronger in order to not let him get hurt again. Black Star and Tsubaki then enter to comfort her. Black Star tries to wake Soul up (rather violently), prompting Maka to give him a Maka Chop. They are soon also met by Medusa (who is disguised as the school nurse) with Spirit who tries to flirt with her (Maka also gives him a Maka Chop). Medusa cheers Maka up by telling her that she will definitely become stronger. Unbeknownst to Maka, Soul's bloodstream is invaded by Black Blood during the fight against Crona and Ragnarok.

Soul Eater Maka Albarn Part in the Story-The New Student and Soul Observation

Maka is seen in class watching the new teacher, Stein, prepare to dissect an endangered bird on the brink of extinction. Tsubaki wonders where Black Star and Soul had got to, and Maka jokingly replies that the two may as well become partners since their attitudes are almost the same, which provokes a shocked Tsubaki to object rather violently towards her. Two students then notice Soul and Black Star about to battle somebody outside. Maka tells Stein that, when two Meisters fight on school grounds, one staff member has to forsee it. With that said, Stein brings Tsubaki and Maka with him. They find that Soul and Black Star are fighting Death the Kid and his partners, who had just enrolled into the DWMA.
Outside, Stein teaches Maka about matching Soul Wavelengths with one's partner(s). Maka witnesses the perfect Resonance between Kid and his Weapons and the imperfect Resonance between Soul and Black Star, using her newly acquired Soul Perception. She watches in dismay as the hapless pair fail to act as a Meister and Weapon and end up being defeated by Death the Kid after trying to execute a sneak attack. However, Black Star and Soul win by default as Kid then loses consciousness after coughing up blood. Maka explains that Soul's sneak attack eariler had cut Kid's bangs, making them asymmetrical, and he had fainted because he had just noticed this. She approaches a battered Soul, and gently scolds him for picking pointless fights, which had been what Soul had told her once before. Soul laughs and admits that he had been 'not cool.' The two agree that Black Star can only be partners with Tsubaki. Maka and Soul agree to work together again as they reconcile.
When Death comes to pick up his son, Kid, Maka takes the opportunity to see his soul. She, however cannot see it and leaves it at that. What she does not know, however, is that the reason she cannot see Death's soul is because it covers the entirety of Shibusen.