The Angels have returned with their third messenger of death, Sachiel, who is laying waste to Tokyo-3, home to NERV HQ, and the feeble resistance put up by the entire UN force present. All of which, however, proves to be of no avail, even the devastating power of the UN's latest addition to their arsenal, the N2 non-nuclear mine, proves to be laughable when faced with the wraith of the Angels. As a result of the UN's ineffectiveness, command of the defence operation is transferred to NERV.

NERV respond to the dire situation by preparing the launch of mankind's last hope for survival; Evangelion, a bio-mechanical giant specialising in close combat and capable of generating its own AT, Absolute Terror, field. EVA-01 is ready, all that NERV require now is a pilot. Only children born in the aftermath of the second impact, exactly nine months after the massacre, have the ability to synchronise with an Evangelion and thus pilot it. The first child was found and underwent the process of synchronising with her Eva, however, the doomed test pilot, Rei Ayanami, lost control of her prototype Eva, EVA-00, in a mysterious accident which left her seriously injured.

All is not lost, however, as a potential new pilot is found, the third child Shinji Ikari, estranged son of Gendo Ikari; Commander and head scientist at NERV. Shinji is picked up by Captain Misato Katsuragi on the day of Sachiel's attack, however, both are caught up in the cross fire between the Angel and the UN whilst enroute to NERV HQ. Fortunately though both Shinji and Misato make it through with only a few scratches and Shinji is brought before his father for the first time in three years.

Despite his reluctance to pilot EVA-01, Shinji finds himself being railroaded into synchronising with the Eva having been alerted to backup pilot Rei's critical condition. The synchronisation process between Shinji and EVA-01 goes surprisingly well, Unit 01 is activated and the battle for Tokyo-3 is set.

Genesis 0:1/Episode 02 - The Beast

Shinji finally awakens, only to find himself staring at an unfamiliar ceiling from a hospital bed, but with no idea as to how he came to be there. He has no recollection of the recent past events, including that of his battle with the third Angel.

Confused Shinji recovers from his ordeal, Misato and Ritsuko Akagi, one of NERV's leading scientists, head up the salvage operation for the battle of Tokyo-3 in which Unit 01 sustained moderate damage. Meanwhile Gendo defends himself and the existence of NERV against extensive criticism from the UN committee who believe that Eva was used inefficiently, and that certain top secret projects associated with NERV are falling behind schedule.

With emotions still running high between Shinji and his father due to past events, Shinji chooses instead to accept the sisterly Misato's invitation to stay with her, despite Ritsuko's dim view of the whole idea. Misato takes Shinji to get his first real glimpse of Tokyo-3, mankind's fortress against the Angels, the city he saved, after which she takes the third child to his new home. It soon turns out, however, that Misato isn't quite the ideal roommate Shinji had in mind.

Later that evening, having drowned his sorrows in the bathtub, Shinji starts to reflect on his stressful first day at NERV. In doing so he abruptly starts to recall the memories of his first sortie in Unit 01; the battle that took place in Tokyo-3, the heavy damage sustained to Unit 01's arm and head component and how it eventually went berserk killing Sachiel in an all out killing frenzy. Now his only comfort are those few words from Misato, telling him to hang in there, as she turns in for the night.