The Romulan military presents the Imperial Senate with plans to ally with the Reman military and launch an invasion of the Federation. However, the Praetor (played by Alan Dale) rejects their cooperation. In a twist of fate, a green Thalaron radiation mist is unleashed in the chamber, resulting in the immediate death of all present. Meanwhile, the crew of the USS Enterprise-E prepares to say goodbye to their longtime first officer, Commander William Riker (Patrick Stewart) and Counselor Deanna Troi (Marina Sirtis), who are set to marry on Betazed. During their journey, they detect a Positronic energy signal from a planet within the Kolaran system, located near the Romulan Neutral Zone.
Captain Jean-Luc Picard (Patrick Stewart), Lieutenant Commander Worf (Michael Dorn), and Lieutenant Commander Data (Brent Spiner) land on Kolarus III and stumble upon the remnants of an android that resembles Data. After reassembling it, they find out its name is B-4 (Brent Spiner), which leads them to conclude it's an earlier, less advanced prototype of Data.
Vice Admiral Kathryn Janeway (Kate Mulgrew) later tasks the crew with a diplomatic mission to Romulus, revealing that a military coup has taken place and the government is now led by a Reman named Shinzon (Tom Hardy), who professes a desire for peace with the Federation and freedom for Remus. This development is unexpected, particularly given the longstanding prejudice held by Romulans against Remans, historically viewed as a labor class.
Upon reaching Romulus, the crew discovers that Shinzon is actually a clone of Picard, a remnant of a clandestine experiment by the Romulans to replace Picard in Starfleet as a spy; however, he was abandoned following a political upheaval and left to a life of servitude on Remus. It is there he joins his fellow Remans and rises to power, constructing his formidable flagship, the Scimitar, equipped with undetectable cloaking technology, an advanced arsenal, and nearly impenetrable shields.
As the diplomatic efforts appear to be progressing smoothly, the crew uncovers that the Scimitar is emitting dangerously low levels of Thalaron radiation, identical to that used to assassinate the Romulan Senate earlier in the story. Complications arise when Counselor Troi faces a psychic assault from Shinzon during an intimate moment with Commander Riker.
Captured by Shinzon, Picard learns he is suffering from accelerated aging due to the cloning process and needs Picard’s blood for survival. In a shocking revelation, Shinzon transports B-4 onto the Scimitar, admitting to orchestrating B-4's placement on Kolarus III to lure Picard. However, B-4, unexpectedly, reveals himself to truly be Data, rescuing Picard and assisting their return to the Enterprise. Understanding that the Scimitar houses a weaponized Thalaron emitter capable of obliterating entire fleets and even planets, Data realizes that Shinzon intends to use it to conquer the Federation, threatening Earth itself.
The Enterprise races back toward Federation territory, only to be ambushed by the Scimitar, which disables their warp drive with its initial barrage of torpedoes. The ensuing battle proves to be very challenging, with the Enterprise struggling against the formidable Romulan Warbirds, all while Shinzon targets Picard and severely damages the Enterprise.
Defiant and unwilling to concede defeat, Picard attempts a desperate maneuver, ramming the ailing Enterprise into the Scimitar, achieving only minimal damage. In a further attempt to subdue the Scimitar, Picard tries to initiate the self-destruct sequence, but it's rendered nonfunctional due to the earlier assault. As the stakes escalate, Shinzon activates the Thalaron weapon in a reckless attempt to destroy the Enterprise along with himself.
Confronting Shinzon aboard the Scimitar, Picard realizes he cannot halt the weapon. In a tense moment, he kills Shinzon into the process of escaping the collapsing vessel, as Data arrives just in time with a personal transporter that safely beams Picard back to the Enterprise, sacrificing himself to take down the Scimitar and deactivate the weapon.
As the Enterprise undergoes repairs post-battle in a near-Earth space dock, Picard bids farewell to the newly promoted Captain Riker (Patrick Stewart), who is set to command the USS Titan and initiate genuine peace negotiations with Romulus. In a poignant moment, Picard then learns from B-4 that Data had transferred the engrams of his own neural net into B-4's Positronic matrix shortly before his sacrifice.
