The film is a direct sequel to the 2002 film, Godzilla Against Mechagodzilla. In that film, Mechagodzilla was built by the Japanese government to defend against Godzilla. The mechanical monster proved successful in defeating Godzilla, and his body was sealed away to prevent it from being disturbed.
In Godzilla: Tokyo S.O.S., the bones of Godzilla are accidentally uncovered during construction, leading Mothra to arrive and warn humanity of the consequences of disturbing the dead. Mothra is a giant moth who serves as a protector of Earth and often battles alongside Godzilla.
Meanwhile, Mechagodzilla is undergoing repairs and upgrades after its battle with Godzilla. The pilots of Mechagodzilla, including protagonist Akane, are conflicted about returning Godzilla's bones to the sea, as they believe using them to further improve Mechagodzilla's capabilities is a better option.
As Godzilla continues his destructive rampage, the pilots are forced to use Mechagodzilla to defend against him once again. Ultimately, they are forced to make the difficult decision of whether to return Godzilla's bones to the sea and risk losing their best defense against the rampaging beast.
The film received generally positive reviews, with praise for its special effects and action sequences. It also marks the final film appearance of actress Yumiko Shaku, who portrayed Akane in both Godzilla Against Mechagodzilla and Tokyo S.O.S.