Setting
The setting of Supreme Commander is a future in which humanity is able to travel through the galaxy quickly using a quantum tunnel, a portal opened in the fabric of space leading to a designated location potentially light-years away. Tunneling let humankind establish many colonies, which were governed by a centralized Earth Empire. As the number of human worlds grew, however, its control eventually weakened, and the Empire collapsed. The Empire's remnants formed the United Earth Federation; a race of cybernetically-enhanced humans seeking independence formed the Cybran Nation; and colonists who befriended and embraced the religion of the dying alien seraphim formed the Aeon Illuminate. The three factions came into conflict, starting the Infinite War. One thousand years later, the events of Supreme Commander take place, ending the war.
Supreme Commander ending
All three endings for the Supreme Commander campaigns feature teaser endings after the credits as a reference to the (then unannounced) upcoming expansion. The Cybran ending shows QAI calling in unidentified enemies, and then to Dr. Brackman's horror, saying "They are coming". The Aeon ending simply depicts Princess Rhianne, the leader of the faction, opening her eyes in shock and exclaiming "No!". The UEF ending shows many unidentified radar signatures appearing near the location of Black Sun on Earth.
Plot
The game takes place shortly after the first game, which ended with the firing of the Black Sun, a powerful weapon capable of firing a beam through the Quantum Gates to destroy enemy planets. The Seraphim, a race long thought to have gone extinct, have exploited the firing of Black Sun to create a rift from the Quantum Realm they inhabit to our universe, on Earth. Once through the rift, they wreak a path of destruction through the civilized galaxy, leaving Earth and most of the core worlds of the UEF in ruins. With most of the UEF's key political and military leaders lost, including General Samantha Clarke who died while fighting on Capella, General Hall and Brigadier General Fletcher lead the last of the UEF Military. QAI, the once-loyal Cybran supercomputer built by Dr. Brackman, has been compromised and is waging war on behalf of the Seraphim. It cripples the Cybran Nation's military, forcing Dr. Brackman and Dostya to retreat to the further reaches of space. The Aeon Illuminate are divided over the arrival of the murderous Seraphim from whom they once learned what seemed the peaceful Way; many take sides with the Seraphim as the Order of the Illuminate, led by Evaluator Kael, and brand Princess Rhianne a traitor and heretic. Crusader Rhiza leads a handful of forces loyal to the Princess in a guerrilla-style campaign. Shortly afterward, the UEF and Cybran factions ally and form the Coalition against the Seraphim, with the Aeon Loyalists joining afterward despite Dr. Brackman's reservations.
Before battle commences in the first mission, the player must choose a faction to swear loyalty to. This can either be the UEF, Cybran Nation or Aeon Illuminate loyal to Princess Rhianne. The overall plot and outcome of the campaign remains the same, although certain commanders respond differently or reveals different information to the player during several places in the campaign.
The game begins with the protagonist defending the Coalition base on Griffin IV, the last major UEF base and last line of defense against the seemingly inexorable onslaught of the Seraphim. Order forces are attacking the base and the player is being gated in to hold the line. After choosing his/her side and helping Fletcher hold back the attacking Seraphim and Illuminate, it is discovered that Princess Rhianne of the Aeon Illuminate, thought to have been killed by the Order, is alive, hiding in her palace. She is rescued by Coalition forces, and is able to organize many disenfranchised Aeon who are troubled by the actions of the Seraphim and the Order. It is also discovered that there is a traitor within the Coalition, who is leaking information to the Seraphim and the Order of the Illuminate. Both the UEF and Aeon focuses on reorganizing their forces while the Cybrans focus on uncovering the identity of the traitor. Cybran forces loyal to QAI are also encountered during several key battles.
During the fourth mission, the traitor is eventually revealed to be Hex5, formerly loyal to Dr. Brackman and Dostya, now serving QAI referred to as "The Master". Ambushed by Hex5, who proceed to kill Dostya, the player is only given a narrow window from which to defend himself/herself against all odds before being recalled. Immediately afterward, the Coalition discovers that the rift from the Quantum Realm is unstable, and that the massive onslaught that has devastated their worlds and from which they are only beginning to push back is merely the first wave. The Seraphim are building a Quantum Arch on Earth to stabilize the rift; once its construction is completed, no one will be able to survive the armada of Seraphim that will flow through it. Thus, the Coalition plans to launch an all-out assault on Earth.
