Hyper Mecha-King Ghidorah's body is more mechanical than the original Mecha-King Ghidorah: while Mecha-King Ghidorah had one robotic head and two organic ones, all three of Hyper Mecha-King Ghidorah are mechanical. In addition, his wings appear to be based more on King Ghidorah's normal wings. His legs also appear to be of the same design of the legs used on the G-Guard MechaGodzilla.
Zaguresu would show herself again. With events beginning to boil down to the final confrontation, she returned in the heart of a new and improved Hyper Mecha-King Ghidorah, and once again tried to conquer Godzilla Island and the world. Soon Landes managed to discover the warp gate buried on the island, and the truth behind the invasion was soon discovered. After the destruction of the final Vabaruda, Zaguresu once again attacked Godzilla Island with Hyper Mecha-King Ghidorah, and Landes attacked in the stolen Gyotengo. However, just in time, the G-Guard Commander's daughter Misato managed to power on the warp gate, and both the Gyotengo and Hyper Mecha-King Ghidorah, as well as their evil pilots, were sucked into the portal, never to be seen again.
- Hyper Mecha-King Ghidorah can unleash an ice breath from the mouth of his middle head.
- Like King Ghidorah, Hyper Mecha-King Ghidorah can also fire Gravity Beams from the mouth of all 3 of his heads except that they're red instead of yellow.
- Hyper Mecha-King Ghidorah can also emit a green tractor beam from the mouth of his middle head.
- Hyper Mecha-King Ghidorah can also eventually re-attach one of his heads whenever it has either severed or blown out.