Under constant attack by monstrous creatures called Angels that seek to eradicate humankind, U.N. Special Agency NERV introduces two new EVA pilots to help defend the city of Tokyo-3: the mysterious Makinami Mari Illustrous and the intense Asuka Langley Shikinami. Meanwhile, Gendo Ikari and SEELE proceed with a secret project that involves both Rei and Shinji.

In an effort to find an economic means of purifying salt water, a joint U.S.-Japanese military command is set up on an isolated Japanese island where an unusual salt water lake is situated. However, their purifying experiments arouse the prehistoric monster Obaki from hibernation at the lake's bottom, and it proceeds to attack Japan. Although made by a U.S. independent film company, this film was based on a Japanese Toho monster film of 1958, "Daikaiju Varan", from which all of the monster effects scenes and a few incidental dramatic shots were edited into it.

Global panic ensues when it is revealed that a mysterious UFO is actually a giant turkey-like bird that flies at supersonic speed and has no regard for life or architecture.

On behalf of "oppressed bugs everywhere," an inventive ant named Flik hires a troupe of warrior bugs to defend his bustling colony from a horde of freeloading grasshoppers led by the evil-minded Hopper.

In 1930s Korea, a swindler and a young woman pose as a Japanese count and a handmaiden to seduce a Japanese heiress and steal her fortune.