Mecha-King Ghidorah is completely under the control of Emmy Kano and M11, and as such does not act independently; he fights only to stop Godzilla. In Godzilla: Rulers of Earth, the Cryogs gain control over Mecha-King Ghidorah by severing his central head and replacing it with a mechanical one operated by the psychic commands of the human twins Minette and Mallory. However, the two organic heads retain some autonomy and eventually allow Mecha-King Ghidorah to break free of the aliens' control. Upon regaining his independence, Mecha-King Ghidorah immediately abandons the battle against Godzilla and Anguirus and flees to outer space, possibly in search of other members of his kind, according to Rhizon.

Mecha-King Ghidorah is the primary villain of the game Godzilla: Domination!, in which he is behind the disruptive energy waves emitted by the mysterious Meteor X, which allows him to control other monsters.