Research points can be spent on faction-specific tech trees to add bonuses, abilities and upgrades, and to unlock more-advanced units and buildings.
As the campaign progresses the player is able to unlock a wider range of units, the missions become more challenging, and the enemy grows stronger.
In an interview with MacGamer, an online magazine dedicated to gaming on Mac PCs, game designer Chris Taylor had this to say about Supreme Commander 2 and its spiritual link to his previous Total Annihilation series: "I think they are indeed the spiritual successors, because of the way I approach RTS Real-time strategy design.
After a botched training exercise and an incident in Coalition headquarters, Maddox fights off rogue Cybran units at a communications array.
After defending a strategic weapons facility and encountering a mysterious Cybran in the Weddell Straits, Rogers orders Maddox to destroy the Illuminate colony of New Cathedral.
After failing to stop UEF Commander Lynch from destroying New Cathedral with nuclear weapons before the population can be fully evacuated, Maddox decides to go on his own mission to eliminate Colonel Rogers.
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, meeting the mysterious Cybran, William Gauge, when they request assistance.
The siblings learn of Maddox's defense of New Cathedral from Gauge and accompany him in his attack on the Coalition center of Quantum Science and Technology, hoping to send a message to the Illuminate government.
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 a Royal Guardian, a Cybran, and Maddox, who has been holding position at the gate since his battle with Rogers.
Dr. Brackman informs Ivan that Shiva Prime is an ancient terraforming device built by a precursor race older than even the Seraphim, and that the component Dr. Snyder had been researching was an advanced propulsion system.
The pair secure Dr. Brackman's research 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, Ivan travels to Altair II, where he encounters Thalia and Maddox holding off a Guardian assault.
In the final cutscene, Ivan gives a voice-over speech at the Coalition Senate appealing for renewed ties between humanity's factions while scenes of Maddox returning to his family and Thalia visiting Jaren's grave are shown.