When a new weather satellite is mysteriously shot down, the team traces the missile's source to an island near Australia. They find the island fortified and under the command of a terrorist organization known as COBRA. The terrorists imprison the team thinking they are spies. The nuclear reactor on the island begins to suffer problems that threaten to cause an explosion that could destroy the island. Godzilla must rescue the team, stop the COBRA group, and prevent the reactor from exploding.

A UFO lands in the Arctic and the team is sent to investigate. They discover a group of ice people from another planet that plan to destroy the Earth with an asteroid the size of the Moon. Majors and Quinn are taken prisoner and Godzilla, Brock, and Godzooky are frozen. Pete must free the others before the asteroid destroys the world.