Three months later, the UEF had also suffered heavy losses. Both the UEF and the remnants of the Cybran forces, having been pushed to the edge of the galaxy and on the edge of defeat, allied and formed the Colonial Defense Coalition, creating a unified command structure to conduct operations. Rhiza and the Aeon Loyalists eventually join the coalition. One year after the Coalition launched its first offensive, it scored its first victory against the Seraphim, despite suffering heavy casualties. Over two years after the invasion began on X-Day, the UEF began construction on Fort Clarke, a new base of operations located on the planet Griffin IV. The first mission of Forged Alliance throws the player right into the fray: Fort Clarke is under heavy assault, and the player must fight to rescue the last UEF stronghold. There are a variety of side missions, which differ between the three factions.
After lifting the siege, the player is sent to rescue the loyalists being held by QAI and Order forces. Dostya suspects there is a traitor in the Coalition, and starts work on a tracking program. After releasing the prisoners, Princess Burke, presumed dead, returns. After defeating QAI, it is revealed that, with the news that the princess has returned, approximately a third of the Order has rebelled against Kael. Dr. Brackman manages to seize a Seraphim support command unit as it is gated in, and starts working on a translator. The question of the Princess' whereabouts is immediately answered in the next mission, and once again the player must launch a rescue operation and secure her palace.
In the fourth mission, word comes that the Seraphim are constructing quantum gates in preparation for a major offensive on Coalition space. Dostya once again reveals her suspicions: First, that the secret location of Fort Clarke had been discovered, and secondly that the loyalist network was compromised. The player is told that the information about this operation was provided by the Seven Hand node. Dostya's suspicions are confirmed when she and the player are stranded on the planet after destroying the gates, with multiple quantum jammers preventing a recall. The traitor is revealed to be Hex5, leader of the Seven Hand node, who kills Dostya after the revelation. Immediately afterward, the player's base falls under heavy assault, and the player must survive until HQ can lock on and provide a means of escape.
It is revealed after this that the Seraphim presence in the galaxy is a fragile one: the rift from where they entered this realm is unstable, and they are constructing a quantum arch on Earth in an effort to stabilize the rift and call for reinforcements. In the fifth mission, the player is tasked with assaulting QAI's mainframe and destroying Hex5, as well clearing the path for Dr. Brackman's Megalith to personally shut down QAI and extract the gate codes to Earth. In the final mission, the player must destroy the quantum arch on Earth, the Seraphim war leader, and remaining traitors. Princess Burke lands on earth and enters the rift to seal it from within.
Completion of the final mission results in a teaser video, after the credits, where QAI appears to reboot stating: "Re-establishing primary CPU algorithms. Primary CPU algorithms operational. All systems online. Diagnostics complete. Primary directive recognized. Executing."