He is seen in the company of the Instrumentality Committee, in a similar cylinder to that which Rei Ayanami was seen in earlier (Volume 6). Keel Lorenz believes that he is their trump card against Ikari.
Kaworu is playing Beethoven’s ‘Ode to Joy’ on a piano in a ruined church-like building when he meets Shinji, who has just found a stray cat. He claims he’s lost and trying to find the school, asking Shinji to take him there. Shinji lets the cat go because he can’t look after it and Kaworu kills it. He introduces himself properly to Shinji and says that he is the Fifth Children. They reach the school and, when Shinji runs away, he seems to change his mind and asks to be shown where NERV is.
He finds his way into the ladies room and tells Asuka that she needs to be open for the Eva to operate. The girl is infuriated and soon faints. After Asuka faints, Misato tells him to leave the premises until he’s needed. His file claims he was born on the day of Second Impact.
When Asuka is attacked by the Tenth Angel, he merely thinks that things have begun to get interesting. With Asuka placed in a coma after the battle, Misato officially assigns him the pilot of Eva 02.
He attends a SEELE meeting and his inability to prevent Ikari’s use of the Lance of Longinus is called into question. He replies that it’s unwise for him to appear there any longer because of his new NERV placement. He reveals that he was told to stick by Shinji by SEELE.
Soon Kaworu meets Rei, telling her that they are the same, but she disagrees. During a synch test later, he stuns the NERV bridge staff when he is capable of synchronising with Eva 02 without the core having been rewritten for him. He later scares Shinji while the latter is showering by walking in on him and asking for some soap. With Rei he is sortied to battle the Eleventh Angel. During the battle his skills are complimented by the bridge crew as being better than those of Asuka’s. He seems to try talking with the angel as well, convincing it that he is the one who survives in the scenario and not the Eleventh Angel.
His Eva is contaminated by the angel, and although he believes he could easily use his own AT Field to expel the angel he also doesn’t want to reveal his true identity as of yet. After the battle he confronts Shinji about his despair at Rei’s apparent death, calling the girl stupid. After Shinji faints, he visits him in the infirmary. Shinji stays with him after Rei’s death, saying that because he’s not grieving Kaworu is the best person for him to be around right now.
Kaworu seems upset when Shinji goes home to Misato’s after Rei is revealed to be alive.
When he encounters Rei after her incident, he tells her that they have both arrived in the forms of humans in order to live on the Earth. He later meets Shinji and tells him that he’s lost everyone he could call a friend except for himself. He walks away when Shinji tells him he couldn’t consider him a friend and asks him to let go of his shirt.
Kaworu meets with SEELE, who mention that Adam’s salvaged soul resides in him. With the meeting ended, he begins to make his move against NERV. Hyuga reveals that Ibuki knew he could set his synch ratio at will.
During his attack he uses Eva 02 to help punch his way down to the giant within NERV headquarters. Kaworu is surprised when Shinji arrives in Eva 01, telling him that he’s late. He reveals that because Eva 02 is born from Adam just as he is, he is capable of manipulating it. When he uses his AT Field to protect himself from the Eva’s attacks, Kaworu explains to Shinji that the AT Field is nothing more than the barrier of the heart.
When Kaworu encounters the giant in NERV headquarters, he reveals that it is actually Lilith and not Adam. Upon making this discovery, Kaworu decides to sacrifice himself and defy his orders from SEELE. He asks Shinji to kill him if he has any feelings for him, just as he had killed the cat when they first met. Shinji squeezes him to death with the Eva’s hands. In his mind, Shinji sees it as himself who kills Kaworu instead of the Eva.
The entry plugs used by the rest of the Eva series have ‘Kaworu’ written on them. It isn't definitively known as yet if there is a greater connection between the Mass-Produced Eva's and Kaworu.