While investigating an ocean volcano, the team find the volcano oozing a strange liquid that causes sea creatures to turn into giants. The team and Godzilla must find a way to get the creatures back to their normal size before they threaten nearby shipping lanes.

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.