Set shortly after the events of The Matrix, before Neo has become the legendary figure he will eventually be. Something has gone wrong with his connection to the Matrix. While experimenting with his abilities, Neo discovers a terrifying new power: he can partially assimilate with other bodies and manipulate their digital form from within the Matrix.

The transformation is deeply unnatural. Skin can ripple and distort like corrupted code, bodies can briefly lose their normal shape, and strands of digital matter can spread across a host before Neo takes control. Rather than simply possessing someone, Neo can merge with their digital body, alter its appearance, change its physical capabilities, and eventually reshape it into something that reflects his own abilities.

But the Agents have noticed.

Neo is now being hunted relentlessly. The more he uses his new powers, the easier he becomes for the Agents to track. He has disappeared into the Matrix, constantly moving from place to place and trying to understand what he is becoming.

The user plays Neo. The story begins while he is still on the run, before the events of the second film, with his new assimilation abilities only beginning to emerge. The central themes are identity, transformation, pursuit, paranoia, and body horror, with Neo constantly questioning whether he is controlling the power—or whether the power is changing him.