It's set some years after the events of Star Trek Nemesis. Nero and the crew of the Narada (at this point a fairly simple Romulan mining vessel) barely escape a gigantic supernova, and quickly head back to Romulus to warn the Senate that they believe this supernova could eventually wipe out most of the Empire, including Romulus itself. Ambassador Spock also believes this is a distinct possibilty, but neither he nor Nero can convince the Senate, whose own scientists believe the nova will die out before it causes any serious damage. Besides, the only known race with the technology to do anything about the supernova are the Vulcans, and the Romulans are not interested in accepting their help.

Nero takes Spock on board the Narada and secretly heads to Vulcan, in order to plead for help anyway from the Vulcan High Council and are joined in this effort by Ambassador Picard and Data (B4 from Nemesis with Data's personality and memories uploaded), who is now Captain of the Enterprise-E. The High Council however are reluctant to provide any help without officially being asked by the Romulans, which causes Nero to head off in a huff to try and save his family before Romulus is destroyed.

Eventually Spock, Picard and Data are able to convince the High Council to allow Spock to take the Jellyfish (Spock's ship from the movie) with the Red Matter to head into Romulan space and stop the supernova (Spock volunteers due to his age - this will almost certainly be a suicide mission). However all of the delays caused by the High Council means that Spock is not able to reach the supernova before Romulus is destroyed. Likewise, Nero also fails to rescue his family in time before having to witness the destruction of his home. As a result, he and his crew shave their heads and tattoo their faces (apparentely a sign of their mourning) and locate the Romulan Senate, who have escaped the destruction in their own ship. He kills the Praetor for failing to do anything to stop the destruction of Romulus, then makes the remaining Senate members give him access to a top secret Romulan weapons research base so that he can outfit the Narada with super-advanced weaponry.

Nero then heads off to intercept Spock and prevent him from stopping the supernova, as he wants it to continue to destroy the Federation like it has the Romulan Empire. However, Spock has already launched the Red Matter by the time the Narada catches up to him and both ships gets sucked through the resultant black hole.