Metal Gear has fallen into the hooves of an Equestrian revolutionary, who, with the backing of his human mercenary allies, intends to use it to depose Celestia and crown himself ruler. Having crossed into Equestria in pursuit of this rogue weapon, the legendary Solid Snake must ally with the residents of Ponyville to prevent a nuclear catastrophe.
See also Equestria Gear Solid, the hilarious spin-off EQG parody in which everything you know is wrong, and every single character from the story is an awful caricature of themselves.