25 years after the
expansion of the first game, the newly elected Coalition President is assassinated, causing the breakup of the coalition formed to defeat the Seraphim. The first phase of the campaign (dedicated to the United Earth Federation, or UEF) follows Dominic Maddox, a UEF officer who is married to an Illuminate. After a botched training exercise, Maddox fights off rogue Cybran units at a communications array. After repelling the attack, his
commanding officer, Colonel Rogers, takes sole command of all UEF forces on the planet. After defending a strategic weapons facility and encountering a mysterious Cybran named William Gauge in the Weddell Straits, Rogers orders Maddox to destroy the Illuminate colony of New Cathedral. Maddox, knowing that his Illuminate wife is inside New Cathedral, refuses and goes
AWOL. Along the way, he is contacted by Dr. Zoe Snyder, whom provides him weapons and technology. After failing to stop UEF Commander Lynch from destroying New Cathedral with
nuclear weapons before the population can be fully evacuated, Maddox decides to eliminate Colonel Rogers. Maddox defeats Rogers' forces and destroys his command center, but destroys the stealth system shielding a hidden teleportation gate in the process, unlocking the second phase of the campaign. The second phase (dedicated to the Aeon Illuminate) follows Commander Thalia Kael as she fights for a group known as the Royal Guardians to "restore the Illuminate to their former glory." After ambushing a Cybran weapons convoy, securing technology from a decommissioned Aeon facility, and freeing a group of Aeon political prisoners, Thalia, along with technical assistance from her terminally ill brother Jaren, defends a geothermal power plant from UEF forces, where they meet Gauge, whom has show up for their assistance. The siblings learn of Maddox's defense of New Cathedral from Gauge and accompany him in his attack on a Coalition outpost, hoping to send a message to the Illuminate government. Only after Gauge levels the entire outpost's city with nuclear weapons does Thalia realize her mistake in unwittingly aiding Gauge's plans to find what he calls "Shiva Prime." On top of that, the Cybran convoy was actually on a humanitarian mission and the prisoners she freed were actually Royal Guardian commanders. Seeking to atone for her deeds, Thalia travels to Altair II intending to turn herself in to Coalition forces, but instead discovers a standoff between multiple commanders and Maddox, who has been holding position at the gate since his battle with Rogers. Maddox attempts to deescalate, but Gauge conducts multiple strategic launches to force the parties into combat. Maddox and Thalia join forces and defeat the other commanders, but Gauge arrives and slips past them into the gate. Acknowledging Jaren's observation that more Guardian forces are likely on their way, Maddox and Thalia divert their attention from Gauge and once again prepare their forces. The third phase (dedicated to the Cybran Nation) begins on the planet Seraphim VII, and follows Ivan Brackman (an experimental
clone of Dr. Brackman), an old roommate of Maddox, who fights under the direction of Dr. Brackman. Dr. Brackman informs Ivan that Shiva Prime is an ancient
terraforming device built by a precursor race older than even the Seraphim. The pair secure Dr. Brackman's research from Gauge, whom has arrived via the gate and leave the planet before responding to a distress call from Dr. Snyder, whose facility is under attack by the Royal Guardians. After Snyder realizes her research has been stolen by the Guardians, Ivan travels to Altair II, where he encounters Thalia and Maddox holding off a Guardian assault. After beating back the attack, Ivan returns to Seraphim VII to confront Gauge. Gauge launches Shiva Prime into the atmosphere and sends a Guardian to the surface stop Ivan, but Ivan succeeds in defeating her in time and teleports to Shiva Prime. Aboard the station, Gauge massacres the remaining Royal Guardians and uses the station's propulsion system to immediately travel to Altair II with the intent of destroying the planet. After a lengthy battle with Gauge and Shiva Prime's automated defenses, Ivan defeats Gauge, but then comes to the realization that as long as Shiva Prime exists, the factions will fight battle after battle for its control. He therefore decides not conform to his father's will, destroying Shiva Prime rather than allowing anyone else to possess it, a decision that greatly disappoints Dr. Brackman. In the final cutscene, Ivan gives a voice-over speech at the Coalition Senate appealing for renewed ties between humanity's factions, while Maddox reunites with his family and an imprisoned Thalia visits the grave of Jaren, whom had succumbed to his illness. In the teaser, Dr. Brackman talks with Gauge - revealed to have survived his fight against Ivan and secretly working with Brackman - and begins a proto-brain initialization sequence, asking Gauge if he is ready for a new adventure. == Demo ==