After the defeat of the final Angel, Shinji Ikari falls into a deep depression. When SEELE orders the JSSDF to make a surprise attack on NERV’s headquarters, Gendo Ikari retreats down into Terminal Dogma along with Rei Ayanami, where he begins to advance his own plans for the Human Instrumentality Project. Eventually, Shinji is pushed to the limits of his sanity as he is forced to decide the fate of humanity.
The story is a alternate ending of the final two episodes of Neon Genesis Evangelion tv series. It follows Shinji and Auska trying to prevent the occurance of Third Impact. Shinji still haunted in the death of Karou Nageisa is pressured in piloting Evangelion Unit-01; where Shinji is in the process of deciding whether or not humanity should continue to exist. While, Seele launches a dreadful attack on Nerv itself and given orders to kill all Nerv personal and aquring Eva-02 and Eva-01 in their hands. Their reason is to prevent Gendo Ikari to use Adam and Lilith to start third impact and gather his true intentions.