The U.N.G.C.C. (United Nations Godzilla Countermeasure Center) recovers the remains of Mecha-King Ghidorah and construct Mechagodzilla as a countermeasure against Godzilla. Meanwhile, a giant egg is discovered along with a new monster called Rodan. The egg is soon found to be none other than an infant Godzillasaurus.

Jiban goes into action to save Yoko and several captured children from Doctor Giba's plot of creating the ultimate lifeform.