Three months have passed and NERV is rebuilding itself and Tokyo-3, while Shinji tries to come to terms with his own feelings and with the people around him. Rei tries to find her identity and her place in the scheme of things. And Asuka has to face synch test with Unit-02 again. Will she have the strength to get through with it?
Commander Ikari has ordered the regeneration of Unit-00, perhaps anticipating a strike from SEELE. But will NERV be ready in time? Will Shinji find the motivation he is searching for? Will Misato and Ritsuko put aside their feelings about Project-E and work for the common goal, or will risk everything in search of the truth? And who is this Agent Nakayima? How will he fit into the equation?