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The manga follows the plot of its film counterpart reasonably closely, but deviates at several points.
The manga is extremely violent, with Godzilla suffering from near-torture against MechaGodzilla during the first fight, including having his eyes ruptured and his dorsal fins torn in half. MechaGodzilla is also given a variety of new abilities, including a powerful move in which he fires his arms at Godzilla after the G-Crusher fails. In the final battle, Mecha-King Ghidorah's programming takes over MechaGodzilla and it attempts to brutally kill Godzilla, despite G-Force wanting to capture Godzilla alive. After Godzilla is revived by Fire Rodan, MechaGodzilla attempts to attach itself to Godzilla and self-destruct.
- MechaGodzilla has many differences from its film counterpart in this manga; It has a long, sharp spike erupting out of its forehead. It also lacks a plasma grenade. In addition, the Garuda lacks its masers, instead opting for two traditional cannons, and can release a hail of grappling cables that are similar to MechaGodzilla's shock anchors.
- This manga shares some similarities with a very early draft of Godzilla vs. MechaGodzilla 2 where MechaGodzilla overrides its programming and turns against its human masters. In this early script, this was due to a computer virus, while in the manga it is due to Mecha-King Ghidorah's programming taking control of MechaGodzilla. This plot device was also loosely used for Kiryu in the film Godzilla Against MechaGodzilla in 2002.