Mutoghidorah is a black, yellow and red King Ghidorah with M.U.T.O. arms that have some Ghidorah scales on them, hybrid M.U.T.O./Ghidorah wings and M.U.T.O. heads with small "V" formations on the top of his head and red patches of skin running down his necks.
After Godzilla, Gamera, and Mothra defeated Bagan and Garasharp, the unnamed alien sent Muto Ghidorah ad his final weapon to defat them. A storm began, and Muto Ghidorah fired his Gravity Beams on Mothra, Godzilla and Gamera, then Gamera used his fireball, then Godzilla fired his Atomic Breath, then Mothra used her thunderbolts. All of these attacks had no effect. Godzilla then threw Gamera at Muto Ghidorah, but to no avail. Godzilla proceeded to rip off one of Muto Ghidorah's two tails, Muto Ghidorah then retaliated with his Gravity Beams, hitting Godzilla and Gamera. Mothra then used her poison stings and Gamera used his fireballs, and finally, Godzilla used his tail-slide kick aiming at Mutoghidorah,however Mutoghidoarah flew upwards, causing Godzilla to accidentally kick Gamera. Gamera fired his ultimate plasma, Godzilla fired his spiral ray and Mothra fired her antenna beams. The combined beams destroyed Muto Ghidorah, and unnamed alien's UFO. The storm caused by Muto Ghidorah's presence fades, and then Toto and Little Godzilla killed the unnamed alien with their beam attacks.
- Gravity Beams: Muto Ghidorah can fire read Gravity Beams which are much stronger than King Ghidorah's
- Muto Ghidorah's stomach his back and his wings are immune to Godzilla's atmoic breath, Gamera's fire, Mothra's poison stings and thunderbolts
- For unknown reasons, Muto Ghidorah's presence causes a storm to occur.