He appears as a student in Shinji’s class who’s been away for week. Toji comes across as an angry individual. His sister was injured in the battle with the Third Angel, and he believes that Shinji should feel responsible for what happened. Even though Shinji apologises, Toji doesn’t accept and decks him.
Some time later he bumps into Shinji again, telling him that he hates him. Shinji invites him to punch him again, and Toji is about to when they’re interrupted by Rei Ayanami.
While in a shelter, Kensuke tells him that he owes Shinji because he decked him after he’d protected them. Together with his friend, he (albeit reluctantly) manage to sneak out of the shelter. Unlike his friend, Toji is disgusted at the sight of the angel and thinks that Shinji starts the battle off losing. He is almost squashed when the Eva is thrown into the hills. Shinji calls for him and Kensuke to enter the Eva so that he can finish the angel off without worrying about them. After seeing the stress Shinji endured facing the angel, Toji’s hatred turned into respect.
After Shinji runs away, Toji wonders how he’s doing. Kensuke suggests he talk to Ayanami, but he reveals that she makes him nervous. He visits Misato’s apartment with Kensuke, looking for Shinji.
Continuing from Volume 2, Toji feels the best way to reconcile with Shinji is for Shinji to deck him in return. Shinji thinks it’d be more fun if Toji was in his debt, and leaves. When Shinji is wondering about Rei’s past, Toji thinks he’s perving on her. Shinji sticks his fingers up Toji’s nostrils to get a reaction from Rei, and considers Toji’s debt paid.
Just prior to the battle against the Fifth Angel at Mt Futago, Toji appeared with Kensuke trying to get a sneak peek at the Eva units.
He wonders if anything has happened between Rei and Shinji, seeing as Rei spoke to Shinji of her own accord. When he first meets Asuka while she’s playing a game, he tries to get a look at her panties. After she kicks the machine in frustration, he complains that her personality is a turn-off. He is later shocked when Asuka is enrolled at his school.
Toji and Kensuke are with Shinji again, with Toji teasing Shinji about his resigned acceptance for the upcoming mid-terms. He decides they should discuss their plans at Shinji’s place, in the hope that they’ll see Misato. He is shocked to realise that Asuka has moved in with Shinji. Kensuke decides to host a party for Misato and Asuka, due to Misato’s promotion and Asuka’s new home, but it’s interrupted by Kaji. Upon seeing Asuka’s sudden niceness in Kaji’s presence he warns the man that Asuka’s hiding a vicious, vulgar and violent personality.
He and Kensuke are held back at school by Hikari to clean up the classroom.
When Toji goes to visit his sister at the hospital, his friend Kensuke tells Shinji that he’s forgiven him for the incident entirely. He is later at school, cleaning with Shinji, and tries to teach his friend how to peek up a girl’s skirts. His first target was unfortunately Hikari Horaki, who frightened him off.
He is chosen to be the Fourth Children and pilot for Eva 03. He is pulled out of class by Ritsuko to discuss his new involvement with NERV. Toji approaches Shinji afterwards, and tells him he was chosen as a pilot and accepted so that his sister could get better treatment. He breaks down, apologising again for hitting Shinji.
As he is about to leave for the start-up experiment, Toji meets Hikari and tells her he’d like to try being friends when he returns. During the experiment, Eva 03 is revealed to be possessed by an angel. He is trapped in the Eva throughout the battle, and Eva 01, whilst under the control of the Dummy Plug system, crushes his entry plug. Toji dies because of his injuries soon after the battle.