On Romulus, members of the Romulan Senate debate terms of peace and alliance from the Reman rebel leader Shinzon. The Remans are a slave race of the Romulan Empire, used as miners and as cannon fodder. While a faction of the military supports Shinzon, the Praetor and Senate are opposed to an alliance. After rejecting the motion, the Praetor and senators are disintegrated by a device left in the room.
Meanwhile, the crew of the USS Enterprise prepare to bid farewell to newly-married first officer Commander William Riker and Counselor Deanna Troi. They discover an energy reading on a planet near the Romulan Neutral Zone. Captain Jean-Luc Picard, Lieutenant Commander Worf, and Lieutenant Commander Data land on the planet and discover the remnants of an android resembling Data named B-4. The crew deduce it to be an earlier version of Data.
Enterprise is ordered on a diplomatic mission to nearby Romulus, where Shinzon has taken over the Empire in a coup and professes a desire for peace with the Federation. On arrival, they learn Shinzon is a clone of Picard, secretly created by the Romulans to plant a high-ranking spy into the Federation. The project was abandoned when Shinzon was still a child and he was left on Remus to die as a slave. After many years, Shinzon became a leader of the Remans, and constructed his heavily armed flagship, Scimitar. The Enterprise crew discover that Scimitar is producing low levels of deadly thalaron radiation. There are also unexpected attempts to communicate with the Enterprise computers, and Shinzon himself violates Troi's mind through the telepathy of his Reman viceroy.
Dr. Crusher discovers that Shinzon is aging rapidly because of the process used to clone him, and the only possible means to stop it is a transfusion of Picard's blood. Shinzon kidnaps Picard and B-4, having planted the android on the nearby planet as a lure. Data reveals he swapped places with B-4, and rescues Picard. They have now seen enough of Scimitar to know that Shinzon plans to use the warship to invade the Federation using its thalaron radiation generator to eradicate all life.
Enterprise races back to Federation space, but is ambushed by Scimitar. Despite the aid of two Romulan Warbirds, Enterprise is heavily damaged. Picard rams Scimitar with Enterprise, crippling both ships. Shinzon activates the thalaron weapon. Picard boards Scimitar alone to face Shinzon, and kills him by impaling him on a metal strut. With Enterprise's transporters damaged, Data leaps the distance between the two ships equipped with an emergency transporter, beaming Picard off the ship, and then sacrifices himself to destroy the thalaron generator and Scimitar with it. The crew mourn Data, and the surviving Romulan commander offers them her gratitude for saving the Empire.
Back at Earth, Picard bids farewell to Riker, who is leaving to command the USS Titan. Picard meets with B-4, and discovers that, before he boarded the Scimitar, Data downloaded the engrams of his neural net into B-4. As B-4 starts singing "Blue Skies", a song Data sang at Riker and Troi's wedding, Picard leaves B-4's quarters, smiling.
