After the events of Tokyo S.O.S., a horrible secret is discovered. Extracted DNA of Godzilla from 3/11/1999 is being used as a bio-formation test to create a new MechaGodzilla (named Berserk) while other sources are used from other kaiju in the past to create an army of Mechas. Godzilla and Kiryu wake up and rise back up to Tokyo to battle the Mechas.