Doctor Doom serves as the initial villain in the Chaos Engine trilogy, which opens with the revelation that Doom has rewritten history so that he is now the ruler of the world, having defeated other villains such as the Mandarin, married to Storm and hunting Magneto as his arch-enemy.

Fortunately, a group of X-Men were outside reality when this rewrite occurred and are dispatched to investigate, which leads to them and the "local" Betsy Braddock (her memories restored by Jean Grey) learning that Doom created this reality through a Cosmic Cube.

However, this cube turns out to be flawed in two ways; not only does use of it to maintain this new world drain the user's life-force so that Doom now appears to be in his eighties or older, but he didn't actually change the history of his world but just "superimposed" another Earth's history onto it.

After Psylocke takes him out of reality after Magneto acquires the Cube, Doom is restored to his rightful age and attempts to stage a coup in the Starlight Citadel, only to be opposed by the X-Men and Magneto.

He is ultimately returned to Earth with his knowledge of how to access the Citadel or create a new Cube removed so that he cannot attempt such a scheme again.