Previously... on Supreme Commander

Three factions: United Earth Federation (UEF), Cybran Nation (human Symbionts with technology implants) and the Aeon Illuminate (descendants of the "golden age" of human exploration who met the alien Seraphim and follow "the way") fight in a distant future in the infinite war. Initially members of the Earth Empire, each faction fights for different reasons and eventually tries to rebuild an ancient Seraphim weapon codenamed The Black Sun.

The Black Sun is a weapon based on a quantum singularity. In the future, humans use a vast network of quantum gates for faster than light (in fact almost instantaneous) travel. Each faction has its own agenda: while the UEF plans to destroy several key Cybran and Aeon planets, the Cybrans plan to hack the quantum gates network to isolate everyone else from interplanetary travel, and finally, the Aeon Princess wants to meld with the quantum gates to bring the message of peace all around.

Depending on the faction you choose, you will finally rebuild the Seraphim Black Sun weapon, and the AI that comes with it (named QAI).

QAI launches the mass destruction attack, and everything seems to be going your way, when...

*tam tam taaaaaam*

And now... the conclusion

The Black Sun was indeed fired, and by doing so the barrier to the Quantum Realm was weakened. Ever since its activation, QAI sent covert tactical data to the Seraphim leader Seth-Iavow. The Seraphim invaded the known world, quickly destroying Earth and killing President Riley. Both Cybran and Aeon were overrun quickly in the following month.

Fort Clarke, the new base of operation found on Griffin IV reunites the remaining human forces, UEF, Cybran and Aeon, as they try to mobilize and push back the invaders.

Meanwhile the Seraphim are still trying to build more quantum gates and bring more reinforcements, since the rift open by the Black Sun is pretty weak.

You have been assigned to defend Fort Clarke, which is under heavy attack by the Seraphim forces. Good luck Commander!