The game begins five years after the relocation to the mines in 2175, and follows Darius Mason, grandson of Martian Revolution heroes Alec Mason and Samanya, the main characters of Red Faction: Guerrilla, who runs a lucrative series of businesses based in Bastion, the underground hub of Colonist activity, including mining, scavenging and mercenary work. Few sane people venture to the ravaged surface of Mars, apart from contractors like Darius and smugglers who transport goods between settlements. Darius is tricked into reopening a mysterious, vast shaft in an old Marauder temple by a fanatical Marauder priest, which awakens a long-dormant race of Martian creatures, causing an Armageddon on Mars. Colonist and Marauder settlements alike are torn apart by the new enemies, and the blame for the whole disaster is placed on Darius, soon inciting several angry colonists to form mobs and attack him in their fury. Now Darius must join the Red Faction to clear his name and save the people of Mars, as his grandfather did before him.
Plot
A group of Cultists, a splinter faction of the Marauders led by Adam Hale, attacked and captured a terraformer that controls the weather of Mars. Red Faction forces, led by Frank Winters along with Darius Mason, made an assault on the terraformer. Unfortunately, Adam, disguised as one of the Red Faction, tricks Darius and destroys the terraformer. The destruction of the terraformer results in catastrophic weather which forces the entire population underground.
Fast-forward to a few years later, Darius now works as a freelance miner along with a Marauder friend named Kara within the town of Bastion. Darius begins to leave Bastion for a job when Kara tells him not to go due to a major storm coming and her having a bad feeling about the job. Mason shrugs it off as nothing to worry about. She then tosses him a Benjamin Franklin medallion which she explains is "suppose sic to ward off lightning strikes" for good luck. When Darius is sent to do the mining job, he becomes trapped in the tunnels. At the same time, he learns that he was tricked again by Adam Hale and the cultists who disguised themselves as archaeologist hiring Mason to open a seal that releases an alien race called the Plague. Which, coincidentally happens to dwell in the same tunnels. After falling off a cliff that left him unconscious for three days, Darius, guided by SAM (Situation Awareness Module), escapes the tunnels into an underground mining colony where he finds the Plague attacking the citizens. Grouping up with survivors and some Red Faction soldiers, he escorts an ambulance convoy to Bastion with the help of a L.E.O exosuit that is found along the way. Darius then arrives at Bastion to discover that the town is overrun by the Plague, with all the injured holed up in the center of town. Darius helps out, only to have them turn on him when they find out that he was involved in the release of the Plague. As he escapes to the surface, the pursuers following him are attack and slaughtered by the alien race. The Red Faction, along with Frank, shows up and arrests him, but are attacked, at which point Darius joins the Red Faction and helps fend off the Plague.
Informed that Hale is involved with releasing the Plague, Frank lets Darius know where the Cultists are hiding. Darius assaults them in a walker with Kara, and discovers Hale trying to tame the Plague. Darius then attempts to kill Hale, but fails. Because of this, he tries to escape in a minecart. Hale pursues Darius with his walker. Eventually the walker is crippled by a landslide. Darius takes out his Magnet Gun to finish Hale by dropping pieces of the ceiling on him, with the result being Hales decapitation. He is then picked up by Kara and escape in a walker to a Marauder city where they hope to learn more about the Plague. They discover a secret entrance that is filled with lava, but it's inaccessible, so Darius and Frank take a barge to the machine used to raise the lava, and destroy it to lower the lava. Darius and Kara then head through the tunnels to find the alien Queen, but Kara is killed when they get out to repair a leg. With Kara gone, he takes a personal vendetta against the Queen. He finds her, and in the fight, badly weakens her. Enraged, she begins her ascent to the surface in order to take it over.
At this point, SAM discovers that the Plague cannot withstand pure air. Hearing this, Darius with the help from the nano forge needs to repair the terraformer to bring back the atmosphere. S.A.M explains due to their underground depth they would have to break surface fast to stop Plague from over running Mars. Mason decides the quickest way to the surface is to latch on one of the Queens tentacles during her ascension. He finds the terraformer that Hale destroyed, traverses its Plague infestation within and repairs it, killing off the Plague. The Red Faction along with Marauder forces soon arrives at the terraformer to secure the area. After a brief conversation with Frank, Mason looks at the terraformer to see the clouds start to dissipate after years of dust storms. A thunderstorm starts to appear off at a distance and sunlight breaking through the clouds. Darius pulls out the Franklin medallion he received from Kara and stares at it. SAM warns Darius of high concentration of radiation coming into the atmosphere to which Mason replies "Easy there genius. That's the sun."
