This story is a sequel to Mega Man X: Paradise Lost

One hundred years ago, the Maverick Hunters finished a war. Mega Stallion X, Zero, and Axl put an end to Queen Chrysalis' Changeling invasion, and freed Equestria, at Zero's sacrifice. Twilight became Princess, and ponies, along with other species, enjoyed tranquility and a utopia.

But something happened. Twilight started abusing her powers, turning to dark magic. She created an army of shadow creatures, killed the remaining Maverick Hunters, and killed the ponies that opposed her rule under pretense of "justice".

Those that escaped swore to free Equestria, and found Zero. Without any memories or knowledge of his survival, he sets out on a fight for freedom. With the Four Guardians of Princess Twilight bent on stopping him, Zero will learn Twilight's truth.