During a session of the Romulan Imperial Senate, the military offers the plans to join forces with the Reman military and invade the Federation, but the Praetor refuses. One senator excuses herself for a meeting, leaving behind a device that releases mysterious radiation into the room, killing the entire remaining Senate. Meanwhile, the crew of the USS Enterprise-E prepares to bid farewell to long time first officer Commander William Riker and Counselor Deanna Troi, who are being married on Betazed. En route, they discover a positronic energy reading on a planet in the Kolaran system near the Romulan Neutral Zone. Captain Jean-Luc Picard, Lieutenant Commander Worf, and Lieutenant Commander Data land on Kolarus III and discover the remnants of an android resembling Data. When the android is reassembled it reveals its name is B-4, and the crew deduce it to be a less advanced earlier version of Data.
Vice Admiral Kathryn Janeway orders the crew to conduct a diplomatic mission to Romulus. Janeway informs Picard that the Romulan government has undergone a military coup and is now controlled by a Reman named Shinzon, saying he wants peace with the Federation and to bring freedom to Remus. This is a surprising development as the Romulans had regarded Remans as an undesirable caste used principally as slave labour and shock troops during the Dominion War, due to their long history of prejudice.
Upon their arrival on Romulus, the crew learns that Shinzon is actually a clone of Picard, following a secret experiment conducted by the Romulans to take Picard’s place in Starfleet as a spy; however, he and the project were abandoned after a political change in the Romulan government left him cast away to Remus as a slave. It is there that he meets his Reman brethren and effects his rise to power. It was also on Remus where Shinzon constructed his flagship, a heavily armed warship named Scimitar, with a completely undetectable cloaking device, an arsenal of weapons, and virtually impregnable shields.
Though the diplomatic mission seems to go smoothly, the crew discovers that the Scimitar is emitting low levels of extremely dangerous thalaron radiation (the same radiation used to assassinate the Romulan senate), several unauthorized computer accesses take place aboard the Enterprise, and Troi is mentally attacked by Shinzon while she is having sex with Riker. Shinzon captures Picard after Beverly has informed him that Shinzon is slowly dying from the accelerated ageing from his cloning process; the only thing that will save him is a full transfusion of Picard’s blood. Shinzon also transports B-4 aboard the Scimitar, revealing that Shinzon was behind the placing of B-4 on Kolarus III to lure Picard to Romulus. However, B-4 reveals himself to actually be Data — he rescues Picard and they make their escape back to their ship. Realizing that the Scimitar is a weaponized thalaron emitter with enough power to destroy all life forms in a fleet of ships as well as an entire planet, Data deduces that Shinzon is using the warship to conquer the Federation and destroy Earth.
The Enterprise races back towards Federation space in accordance with orders from Starfleet to rendezvous with other starships, but is soon ambushed in the Bassen Rift (a region which disrupts subspace communications) by the Scimitar, disabling the Enterprise’s warp drive in the process. In the ensuing assault, the Enterprise is outmatched and unable to call for help. Two Romulan warbirds arrive and assist the Enterprise in the battle (the Romulan military having realised they will be held as complicit in Shinzon’s genocidal plans), but Shinzon destroys one warbird (a piece of whose starboard wing hits the Enterprise) and disables the other. Refocusing his attention on Picard, Shinzon further damages the Enterprise.
Refusing to surrender, Picard uses his heavily damaged ship to ram the Scimitar, causing moderate damage including disabling the Scimitar’s disrupter banks. Shinzon then initializes the Scimitar’s thalaron weapon in a desperate attempt to take the Enterprise down with him. Picard boards the vessel alone and faces Shinzon. Unable to prevent the weapon’s activation, Picard kills Shinzon by impaling him through the abdomen with part of a metallic support strut. Data arrives with a single-use personal transporter, using it to quickly beam the Captain back to the Enterprise before destroying the ship at the cost of his life, shutting down the weapon in the process.
While the severely damaged Enterprise is under repair in a space dock in Earth orbit, Picard bids farewell to newly promoted Captain Riker who is off to command the USS Titan, to begin a true peace negotiation mission with Romulus. Picard then meets with android B-4, whereupon he discovers that Data had succeeded in copying the engrams of his neural net into B-4’s positronic matrix not long before his death.