The FedCom Civil War engulfs Kentares IV after William Dresari, a nephew of famed Clan War hero Duke Eric Dresari, betrays the family, launching a surprise attack by Steiner forces on the Dresari royal palace. William seizes the throne for himself under the banner of Katherine "Katrina" Steiner-Davion's Lyran Alliance and became responsible for the annihilation of loyalists to Victor Steiner-Davion. The betrayal leaves Eric Dresari and the majority of the royal family dead.
Upon hearing of the coup, Eric's son, Ian Dresari, returns home and meets up with his uncle, Sir Peter Dresari, on the moon orbiting Kentares to launch a guerrilla campaign to take back Kentares IV from the Steiner loyalists. Ian fights alongside with fellow Resistance MechWarriors Casey Nolan, Jen McQuarrie, and Jules Gonzales, and their commander Elise Rathburn in various missions. The Resistance abandons its base on the moon and sets up camp for the first time in Kentares' arctic regions. At one point during this campaign, Ian's uncle Peter is murdered by Duncan Burke, a high-ranking officer in Katrina's forces. Ian and the rest of the Resistance are devastated by the loss of his uncle and debate over whether or not to continue the fight for Kentares' freedom. They decide to push forward and manage to capture a satellite network from House Steiner. The rebel group moves into the mountains.
After destroying a disabled, but heavily guarded Steiner DropShip, Ian and the resistance move to the Hadra Peninsula, a remote desert region. Rumors of an abandoned prison camp reached the resistance and efforts are made to locate and liberate the camp in order to enlist more personnel for the Resistance cause. Along the way, Ian is shocked to find that one member of his family survived Steiner's siege of the Dresari palace: his sister Joanna. After a short reunion, Ian and Joanna are separated once more as the Resistance plans to mobilize their forces to take the fight to Steiner. While in Hadra, Ian kills James Kulin, who was tasked with suppressing the civilian population of Kentares and personally gave the orders to execute Ian and Joanna's family. They make a brief detour to save a coastal town named Vale after Steiner threatened to bomb the town due to allegations of links to the Resistance. Not only does the Resistance save the population, but Ian manages to personally defeat his uncle's murderer, Duncan Burke, in a heated duel.
Pushing forward into urban environments, the fighting heats up and the Resistance's casualties mount. Joanna informs Ian of an old armory cache hidden somewhere in the city full of equipment enough to outfit four heavy lances of 'Mechs - valuable for assaulting the Dresari palace, now the headquarters for the Steiner occupation. Before the search for the cache could be conducted however, Joanna and her lance are ambushed by Steiner forces, leaving her badly injured and in mortal danger. Ian has to make a choice, between rescuing his sister from certain death or securing the weapons cache for an assault on the Dresari palace. Whatever the player chooses, Ian and the Resistance fight one last battle against House Steiner, finally putting an end to the war. However, the fight is not yet over for Ian, as William shows up in a modified Daishi, challenging Ian to a duel. Ian defeats William and finally frees the planet from Steiner's grasp.
Depending what choice the player makes during the second-to-last mission, either Joanna or Ian will ascend the throne as Duchess or Duke, respectively.