The Seraphim were first discovered by Dr. Jane Burke in a deep space exploration mission. The Seraphim showed the explorers something they called 'The Way'. The Way is an ancient philosophy, promising purification through life. The Earth Empire sent envoys to make sure these "aliens" didn't spread, but the leader of the envoy decided to eradicate the Seraphim after a misunderstanding in negotiations, and called on the remaining colonists to eradicate the alien presence. Smith's forces were out matched by far in firepower, but they released a virus in a last ditch effort designed to kill any Seraphim on the planet. Dr. Jane Burke and the other human disciples of the Way, sent a message to the Earth Empire years later inviting them to share in the philosophy of the Way. The Earth Empire sent military forces to Seraphim II, and the chance of peace with the Empire was shattered. This act of war sparked the beginning of the Aeon Illuminate faction, fighting to cleanse the galaxy through the teachings of The Way. After the Earth Empire's attack the Seraphim are presumed extinct.
The Seraphim begin invading with an invasion fleet beyond anything seen by any human being ever born at the beginning of Supreme Commander: Forged Alliance. The UEF, Aeon, and Cybran nations 'forged' an uneasy alliance, becoming the Coalition, with goal of fighting back against the Seraphim, Order of the Illuminate, and QAI. After the events of Forged Alliance, the Seraphim are presumed to be gone from the galaxy.
For a more in depth look, Seraphim on SupCom wiki.
Supreme Commander 2Edit
Their demise at the end of Forged Alliance meant that they would not make an apperance in Supreme Commander 2 however; there is a kind of easter egg after the end credits.
William Gauge is seen at Dr. Brackman's secret laboratory in front of Dr. Brackman and, what is percieved as being, a Seraphim brain. After the argument of undertaking the 'process', Dr. Brackman is believed to be seen merging his own brain cells with that of the Seraphim brain, sparking debate of the Seraphim returning in the next Supreme Commander game.