In Godzilla vs King Ghidorah, the three-headed dragon was defeated by the reborn Godzilla in their first battle. King Ghidorah lost his middle head, suffered severe damage to his wings and ended up at the bottom of the ocean, leaving the enraged Godzilla to begin a new rampage. King Ghidorah remained at the bottom of the ocean some 200 years into the future, still alive but in a comatose state. Emmy Kano, a time-traveller who unwillingly helped create King Ghidorah, requested that she be allowed to help save her ancestors from Godzilla, and thus King Ghidorah was reborn as a cyborg, Mecha King Ghidorah, and sent back to 1994 to fight Godzilla, with Emmy at the controls. After an lengthy battle, Mecha King Ghidorah took to the air, carrying Godzilla, and plunged into the ocean, Emmy escaping later in a shuttle. Unfortunately, it would take more than that to bring Godzilla down, and he defeated the damaged Mecha King Ghidorah underwater. Mecha King Ghidorah's body would not go to waste however, as his cybernetic parts were retrieved and used to build Mechagodzilla Mk II, whose components in turn would be used in the construction of MOGUERA.

Mecha King Ghidorah is capable of everything he could do as King Ghidorah, with some noted additions. His middle, cybernetic head is equipped with lightning breath, like his organic counterparts, though his is green as opposed to yellow. His chest contains a large claw, which he used to hold Godzilla in place before shocking him into submission with extendable cables. His wings are solid metal, enabling him to fly again, and he is also equipped with a limited supply of small missiles, not to mention the fact that a small one-person cabin enables the monster to be controlled to some degree without alien influence, as is often seen in the Godzilla franchise.