The Hammer Sub was created by the Vortaak and deployed into an ocean. In the Undersea Battle mission, Godzilla must swim to the bottom of the ocean and destroy the alien submarine. It fires torpedoes and lasers at Godzilla. To destroy it, Godzilla must fire at various ares on the submarine with his atomic breath. Each time the sub is hit in one of its vulnerable areas, its health decreases, and the sub sinks once its health is completely depleted.
- The Hammer Sub can fire torpedoes of varying sizes from several different compartments.
- The Hammer Sub is able to fire lasers from beam discharging devices mounted on either side of its hull.
- The Hammer Sub is able to deploy autonomous drones from a compartment in its underside, which are themselves able to fire small, purple energy blasts.
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