Two years after the final battle, humanity still survives. The metropolis of Tokyo-3 was spared the destruction of the horrid Impact, but members of NERV have been counted among the final death toll. However, the survivors managed to rebuild the headquarters and most importantly the humanoid robots Evangelions for a new generation of pilots to man...

Now that the NERV headquarters is completely rebuilt, the quest for new pilots has started. One has been created, much like the former Ayanami Rei, and has been dubbed Azayaka. One has been found, Tobias Shade, and has been sent from America to Japan for his piloting duties. Sohryuu Asuka Langley, only recently awoken from a coma following the Impact, fears a return to piloting. Hoping to pull her from this, NERV sends for one of her old friends, Kaji Shikibu, the younger sister of Kaji Ryouji. Shikibu, a psychologist by trade, returns to Tokyo-4 still bitter from the death of her brother and dragging along with her her German fiance Noah Mueller, who slips into NERV as the new chief medical of the base.

Only days following a new angel attack on Tokyo-4, the entire headquarters of the Filipino branch of NERV in Manila is destroyed by one of the angels. With only one pilot named Hyueh, a tactics expert named Aya, and a handful of technicians remaining from the attack, the survivors move to Tokyo and the headquarters of the entire operation. Katsuragi Misato and Akagi Ritsuko emerge for meeting these new members of the Tokyo base, Ritsuko finally at peace with her late mother and Misato suffering from a lower alcohol threshold. Horaki Hikari, Asuka's former schoolmate, has reluctantly returned to Tokyo as Dr. Mueller's assistant and seems so bruised by her past that she only communicates with Noah. So, what does God have in store for humanity now?

Note: Created characters are permitted and appreciated. No more pilots will be accepted.