The story begins with Niobe, captain of the Logos, and Ghost, her first mate, retrieving a package left in the Matrix by the crew of the recently destroyed rebel ship Osiris. After being pursued by Agents, Ghost and Niobe escape from the Matrix with the package, which turns out to be a message to the human city Zion, warning them that the machines are approaching with an army of Sentinels. Niobe and Ghost are tasked with calling the rest of the ships back to Zion to coordinate a defense.

Welcome to Mega-City One, a city of over 400 million people - every one of them a potential criminal. It is the third decade of the 22nd Century, unemployment is widespread, boredom is universal and only the Judges can prevent total anarchy. Empowered to dispense instant justice, they are Judge, Jury and Executioner all in one. The most feared and respected of all the Judges is you, Judge Dredd.

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.