After achieving the canonical ending, your protagonist wakes up in Doc's office. Something is wrong. They've been here before.
They eventually theorize they are in a simulation or dream. Some sick mother fucker is making them experience the horrors again, and it seems this omnipotent being wants them dead. New threats exist where there were none. Everything looks a bit different, sharper. When they prevail, the being gets desperate. This not of this world start appearing. Dragons, aliens, anthropomorphic Choo Choo trains. Will they survive? Is God playing games with them? Are they even real?
(TL;DR Mod your game to hell and back with no regard for canonical consistency and your protagonist is aware of the discrepancies and has to deal with them while having prior knowledge of this world and it's major plot points)