In the fairly distant future, humans have escaped beyond the confines of their native planet after a mysterious, cataclysmic event has left it crawling with otherworldly ghost-like creatures and left it a place where time and space have come ever so slightly unraveled. With colonies on Venus, Mars, the moons of Jupiter, and hundreds of massive space stations throughout the solar system, Earth is now little more than a planet sized graveyard and a nostalgic memory.

The main character of the game's story, known simply as Rook, is an aged convict aboard an Alcatrez-esque orbital prison station called the VC Harlegand. The Harlegand is stationed in the now isolated corner of the galaxy around Earth, making escape a nearly impossible prospect.

After the prison crash lands on the Earth's surface for unknown reasons, Rook is awoken from a prisoner stasis pod by a friendly hacker and fellow prisoner named Jin who's jacked into his neural implants remotely from a security room in the prison's central tower. Unfortunately, as a death row prisoner who was never intended to be fully resuscitated, upon waking Rook finds himself suffering from fragmented memory, recurring hallucinations, and painful migraines. The prison's medbay can ease his symptoms, but Jin need's Rook's help to reactivate it.

Proposing a plan to escape the planet, she suggests the two work together towards a common goal of survival. The duo embark on a journey to gather what she needs for them to escape, which entails traveling to each of the cell blocks that detached and scattered across the Earth's surface when the prison crash landed. Along the way they'll befriend fellow survivors, clash with gangs of dangerous criminals and monstrous creatures, and unravel the mysteries of the Earth's nebulous fate.