Though Godzilla looks nearly the same in this film as he did in Godzilla 2000: Millennium, this movie takes place in a separate continuity from the previous film. The Godzilla in Godzilla vs. Megaguirus attacked Tokyo in 1954, the Tokaimura Power Plant in 1966, and Osaka in 1996.

In 2000, Godzilla would be the first to encounter the Meganura threat. However, shortly after this, Godzilla would be lured to KiganjimaIsland where he would fall victim to a top secret weapon, the Dimension Tide.

The attack would be interrupted by the Meganura allowing Godzilla to battle their queen, Megaguirus in battle. After Godzilla's victory he would fall victim once again to the Dimension Tide and be buried deep underneath the city. Shortly after the credits, however, the main character (a child) goes to the window and hears Godzilla's famed roar.