Kaji accompanied Asuka to Japan and presents Adam, in cryostasis, to Gendo in secret. Kaji is aware that Adam is the key to Keel Lorenz’s Instrumentality Project. He is next seen interrupting a small lunch being had by Shinji Ikari, Rei Ayanami and Misato Katsuragi with Asuka, surprising Misato with a hug. Although Misato doesn’t act pleased to see him, he does surprise Shinji by knowing his name and of his battles with the angels.
He soon reacquaints himself with his old college friend Ritsuko, mentioning she’s still a workaholic. Perhaps aware that Misato wouldn’t accept his feedback, he uses Ritsuko to feed her an idea after the Seventh Angel fiasco while he looks after Asuka and Shinji. His plan involves teaching Shinji and Asuka to dance as a way to move in perfect harmony, and tells the protesting pilots he chose the music and did the choreography.
When the training he designed doesn’t seem to be working as well as planned, Misato asks Rei to step in. After Asuka saw Shinji and Rei performing in harmony she flees, causing Kaji to nudge Shinji into following her. He is seen shortly after smoking and talking to Ritsuko and Misato about their lack of progress. That night he tries to put the moves on Misato, but is rejected based on Misato’s feelings towards their past relationship. He is on the bridge throughout the battle the following day, and is hugged by Misato when Asuka and Shinji win. He is slapped when she realises what she did.
Kaji is seen entering an abandoned building, attempting to find out the truth about the Marduk Group. He appears to have been followed by Gendo. Upon his return he crashes Kensuke’s celebration party with gifts from Matsushiro. He is still at Misato’s place after the party’s finished, helping Misato due to her drunken state. They talk about their past relationship briefly, indicating that it was a long distance relationship. They lean in to kiss, but Asuka interrupts them.
He is next caught in the blackout with Misato, trapped in a lift. During the time they spend trapped in there, Kaji admits to Misato that if he were to die he wouldn’t regret it because of the time he had spent with her. As the power returns the pair fall into an awkward position, made all the worse when the doors open.
Misato later approaches him at gunpoint outside Terminal Dogma, noting that he is both an agent for NERV and the Japanese Ministry of the Interior. He tells her that Gendo Ikari is aware of this as well, and decides to show her a secret being kept from her by both Ikari and Ritsuko – Adam, who is the basis for Project E and the Instrumentality Project.
Kaji drives past Shinji in a car and offers to talk to him more about the Adam giant and other secrets of NERV, taking him to an aquarium. He tells Shinji that the reason the Angels attack Tokyo-3 is because NERV knew that they would.
He speaks with Misato about the Fourth Children’s discovery, telling her that the Marduk Group is only a front for NERV. As soon as Maya walks in, he begins flirting on her and offering her coffee. Kaji is later approached by Asuka who tells him she loves him, and he is shocked when she takes her shirt off. He tells her that, speaking as an adult, he can’t return her feelings. He denies that Misato is the reason he can’t love her, and is somewhat apathetic when Asuka discovers that Toji is the Fourth Children. Kaji is present at Matsushiro when Misato regains consciousness after the battle against the Eva 03 angel.
After Shinji regains consciousness in the hospital, Kaji is there to take him to see his father. He later finds Shinji during the Ninth Angel’s attack and takes him to a safe place so that he can talk some more with Shinji. He reveals that in the aftermath of Second Impact he and his brother, along with five others, stole what they needed to survive. When they started looting a military base they were found out, with only Kaji being left alive. He tells Shinji he didn’t buy the meteor cover story and desired to seek out the truth, which is the reason he started spying on NERV.
Kaji tells Shinji that just as he survived by sacrificing his brother, so too did Shinji by sacrificing Toji and that neither of them deserve happiness. He watches as Eva 01 digests the Ninth Angel, musing that SEELE won’t be capable of silence after the battle. Meeting with Gendo and Fuyutsuki later, he wonders how the men will explain events to SEELE. Upon hearing that Eva 01 will be shut down, he briefly mentions that Shinji is still inside the Eva.
Kaji approaches Asuka during the salvage operation asking if she’s worried about Shinji, saying that everyone is. He tells her that if she can’t be honest with her feelings she’ll never have a boyfriend and leaves to see Misato. When she asks him about the Instrumentality Project and Adam, he kisses her. After she pushes him off, he’s forced out of the room. He mentions that it’s their eighth anniversary and that he still loves her before he goes.
Shinji sees an image of Kaji in the Eva, trying to convince him to return.
Soon after the salvage procedure, Kaji abducts Sub-Commander Fuyutsuki for SEELE in order to find the truth. Realising that NERV is closer to it than SEELE, he also helps Fuyutsuki escape. He is later shot, but his gunner is left off-panel.
Before he died, he left Misato a message on her answering machine. He told her that she now had the truth, contained on a device he slipped into her pocket when he kissed her earlier.