Originally built as a means to melt enemy tanks and other armored fighting vehicles, the M6000 Thunder Control System would instead be utilized against a much more formidable opponent. As the towering behemoth known as Godzilla was en route to reenergize via nuclear reactor, bulldozers heaved earthen loads to bury ion producing mines. Nighttime fell and a rainsoaked battlefield hosted the likes of military might that could only be challenged by atomic fire. Peppering the battlefield and illuminating the night, monster met machine in a barrage of chaos that soon gave way to careful optimism. Godzilla's feet descended heavily on the landmines and an ionic reaction of thunderous proportions generated artifical lightning to wreck havoc on the seemingly unstoppable menace.

With the Anti-Nuclear Energy Bacteria finally starting to take effect in Godzilla's warming body, the Self-Defense Force desperately threw everything they had at the walking symbol of nuclear devastation in the hopes of restraining his movement to the containment area. The plan had the early signs of success, as the monster was forced from one mine to the next. Before the final stages of Godzilla's defeat could be realized, the nuclear saurian regained his dominance and destroyed many of the mercilous machines that prevented his escape. Men and materiel were swept up in the fierce rage of the roaring reptile. To top it off, the M6000 T.C.System was soon thereafter rendered inoperable by the return of the botanical beast Biollante, her spores somehow preventing the massive array of cathodes and anodes from functioning properly. After the ensuing altercation between Godzilla and Biollante, the machine was back online. Its final useage in that battle was the disintegration of the Saradian agent known as SSS9, a mover of events who had, in a sense, indirectly caused much of the recent devastation that the M6000 was deployed to combat.