The story picks up after the first game ending, where Tom, Luke and Helen escape to Mars with fake IDs, and Tanya remains on Earth to fight Nanotech, the company lead by Richard Meier.

The game is told from four different point of views:

- Luke, who is on Mars with his friends but he can't stop thinking about Tanya and what she told him

- Tom, who is on Mars too, but he has strong unconfessed feelings for Helen, Luke's girlfriend

- Tanya, who decided to stay on Earth to fight against Richard, but will she be able to do it alone?

- Tina, a honest police officers who has strong suspicion about Nanotech and wants to investigate.

Each character choices will change the outcome of the story.