After the terrorist organization known as the Human Liberation Front claims responsibility for blowing up the Megatech Body Corporation building, Section 9 is sent to resolve the situation. Section 9 is able to trace the terrorists' communications and find their location in the bay area; however, it is a trap. Chief Aramaki later announces that the leader of the Human Liberation Front is a mercenary known as Zebra 27. Ishikawa then reports that the Energy Ministry is interested in files relating to Zebra; Aramaki orders further investigation.

On Mars in the year 2080, five years after the events of Red Faction, the nanotechnology developed by Axel Capek, the head scientist of the Ultor Corporation prior to its fall, has been claimed by the Earth Defense Force (EDF). With this technology, the EDF commences a reorganization of the Ultor Corporation with a particular focus on enhanced supersoldiers and suitable weaponry. However, the research that was done by Capek in his laboratories has been consequently stolen by other militant groups and assorted terrorist organizations. This has gone on for years; the research has changed hands in the criminal underworld many times. The player is introduced to their role as an explosives expert (codenamed "Alias") as he embarks on a special operations mission to claim the research data for the Republic of the Commonwealth.