The storyline references several media in the Star Trek universe, incorporating plot elements from television shows Star Trek: Deep Space Nine and Star Trek: The Next Generation as well as the then-recently released film Star Trek: Insurrection.
Following the Dominion War, the Federation turns to rebuilding. However, a Federation timeship, the USS Premonition, suddenly appears from the future, under attack by the Borg. Captain Jean-Luc Picard, commanding the USS Enterprise-E, comes to its aid. The Premonition's captain, Thaddeus Demming, warns Picard of an upcoming Borg invasion. Picard then repels an initial Borg attack on a Federation outpost.
Elsewhere, Commander Worf assists in the defense of the Ba'ku homeworld from the Son'a, after which he is informed of the Enterprise's discovery. While traveling through a hazardous sector of space on his way back to Qo'nos, he is ambushed by his old enemy, Toral, who plans to use a fake Sword of Kahless to take over the Klingon Empire. Toral ambushes Chancellor Martok following another Borg incursion, and another Klingon civil war ensues. After a climactic battle over the Klingon homeworld, Toral is defeated. He retreats to the Neutral Zone, revealing that he was getting assistance from the Romulan Star Empire. Hostilities ensue between the Klingons and the Romulans.
The Romulans, in the meantime, come across a stable Omega Particle, a source of nearly limitless power. The particle, discovered first by a Ferengi mining guild, is about to be sold to the Cardassians; the Tal Shiar sends Admiral Sela to secure it before that happens. Sela captures the Omega Particle and, despite some Borg interference, delivers it to a fortified Romulan base. She then allies with the Borg promising the particle after they destroy Toral's remaining forces, but she then betrays and attacks them after Toral is defeated.
The Borg, wanting to secure the particle at all costs, assimilate a Dominion cloning facility and use it to clone Locutus, the former title of Jean-Luc Picard when he was assimilated. With Locutus leading their armada, the Borg take the Omega Particle from the Romulans and assimilate Ambassador Spock, who is trying to mediate between the Klingons and Romulans. Without him, the two empires go to war, and the Borg are able to enter the Sol system. Locutus and his armada defeat the Federation fleet, kill Worf and Demming, and assimilate Earth. However, Picard and the Enterprise manage to escape through a temporal vortex created by the Premonition.
Going back in time, the Enterprise prevents Spock's assimilation. Picard and Spock are able to forge an alliance among the Romulans and the Klingons, and together the three governments repel the invasion of Earth. The unified Klingon, Romulan and Federation forces push the Borg out of the Alpha Quadrant and capture a Transwarp Gate which they take to Unimatrix One, at the heart of the Borg Collective. There, they discover the Omega Particle is fueling the Borg war machine. The combined force destroys the Omega Particle, but Locutus travels back in time before he can be defeated.
Back in time, Locutus, in a Borg Sphere, tries to kill Picard aboard the USS Enterprise-D shortly after the Farpoint mission. However, Locutus is thwarted by the USS Premonition which, unaffected by the changes to the timeline, pursues Locutus back in time and destroys his ship. When a battle-weary Premonition returns to the "present" and witnesses that all has returned to normal, Demming sends the ship and crew home to a brighter future. The game ends with a final log entry from Picard, noting the departure of the Premonition, as well as the potential disintegration of the Klingon-Romulan alliance, though Picard notes that 'whether the peace will last or not, only time will tell'.
