SEELE orders an all-out attack on NERV, aiming to destroy the Evas before Gendo can advance his own plans for the Human Instrumentality Project. Shinji is pushed to the limits of his sanity as he is forced to decide the fate of humanity.
A ship runs aground on a mysterious atoll leading to an investigation by insurance representative Kusanagi, who discovers an ancient bead that he gives to his daughter Asagi. Meanwhile, ornithologist Nagamine investigates reports of a new species of large bird named Gyaos. As the Gyaos begin to attack, an ancient guardian with a bond to Asagi emerges.
With the Gyaos re-emerging, Gamera's ties to humanity have been severed with his bond to Asagi broken. Nagamine and Asagi investigate while an orphaned girl named Ayana discovers a new creature she names Iris. Nagamine and Asagi must reach Ayana before she takes her revenge on Gamera, who she blames for the death of her family.
