The Romulan military offers the Imperial Senate plans to join forces with the Reman military and invade the Federation, but the Praetor refuses to cooperate. A green thalaron radiation mist is released into the room, and everyone is killed. Meanwhile, the crew of the USS Enterprise-E prepares to bid farewell to longtime first officer Commander William Riker and Counselor Deanna Troi, who are soon to be 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 labor, due to their long history of prejudice.
Upon their arrival on Romulus, the crew learns that Shinzon is actually a clone of Picard, a remnant of 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 completely undetectable cloaking devices, 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 substance used to assassinate the Romulan senate as seen in the film's beginning), several unauthorized computer accesses take place aboard the Enterprise, and Counselor Troi is mentally attacked by Shinzon while she is making love to Commander Riker. Picard is captured by Shinzon and is informed that he is slowly dying from the accelerated aging from his cloning process, and thus needs Picard's blood to live. Shinzon also transports B-4 aboard the Scimitar, revealing that Shinzon was behind the placing of B-4 on Kolarus III in order 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, but is soon ambushed by the Scimitar, disabling the Enterprise's warp drive in the process in her first volley of torpedoes. In the ensuing assault, the Enterprise is outmatched. Two Romulan Warbirds arrive and assist in the assault, but Shinzon destroys one Warbird and disables the other. Refocusing his attention on Picard, Shinzon damages the Enterprise to a significant degree.
Refusing to surrender, Picard uses his heavily damaged ship to ram the Scimitar, but only succeeds in slightly damaging it. Picard even tries to initiate the Enterprise's self-destruct sequence, but finds it disabled from the attack. Meanwhile, Shinzon 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 stop the weapon from activating, 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 sacrificing himself to destroy the ship, shutting down the weapon in the process.
While the severely damaged Enterprise is under repair in a space dock in near-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 learns that Data had succeeded in copying the engrams of his neural net into B-4's positronic matrix not long before his death.
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