On Romulus, the senate is locked in heated debate. Romulus and her sister world Remus are divided, but the Reman leader, Shinzon, has a plan to unite them. Shinzon's plan is rejected, and the senate moves on to other matters. A mysterious device sits on one desk ... and suddenly opens, filling the senate chamber with a strange, green energy. Suddenly, light begins to fill the room and everyone inside groans with pain as their flesh decays. Within seconds, the entire senate is dead.

Meanwhile, Captain Jean-Luc Picard is presiding over a particularly joyous event: a party celebrating the wedding of William Riker and Deanna Troi. As best man, Picard offers up a toast, and complains that everything around him is changing — Riker is leaving for his own command, the Titan, and Troi is joining him. Data will be taking over as first officer of the Enterprise. As everyone wishes the happy couple well, Data serenades them with a rendition of "Blue Skies." Afterwards, the Enterprise heads to Betazed, where the crew will participate in a traditional Betazoid wedding (which makes Worf very nervous). En route, Worf notices a positronic signal emanating from the desert-like planet of Kolarus III. As only Dr. Soong-constructed androids like Data emit a positronic signal, Picard orders the ship to re-route for further investigation.

Data, Worf and Picard head down to the planet with the Argo, a shuttle with a special, dune buggy-like vehicle, in tow. They soon discover various android-like body parts, one of which is a head that looks remarkably like Data. Their mission is interrupted by the natives of Kolarus III, who chase the landing party back to the shuttle. Back on the ship, Geordi La Forge concludes that the android has similar internal mechanics as Data, but is not as developed. La Forge deduces that this one is a prototype. The head introduces himself as "B-4." Hoping to aid B-4's development, Data downloads his memory engrams into B-4's matrix. B-4 doesn't seem to be assimilating all of this new information, but La Forge suggests that Data merely give it some time.

Later on, Admiral Janeway orders Picard on a mission to Romulus. The new Praetor, a Reman named Shinzon, has requested a Federation envoy. On the way to Romulus, Data briefs the crew on the Remans, noting that due to high temperatures on one side of their home planet, they live on the dark side and avoid the sun. It is also noted that the Remans have a reputation as warriors — during the Dominion war, some of their troops were used as cannon fodder.

Once they arrive at the designated coordinates, the crew of the Enterprise is kept waiting for 17 hours. Finally, a massive battleship called the Scimitar uncloaks. Shinzon's Viceroy tersely informs the crew of where they are to transport. Once inside the dark, shadowy vessel, the crew meets Shinzon — and he's human. He also seems particularly interested in Troi, as he has never seen a human female before. Picard wants to know what this mysterious new Praetor wants, but Shinzon will only reveal that he desires peace and unity. Shinzon then raises the lights, and Picard is shocked to see a familiar face staring back at him. Shinzon reveals that he has a rare syndrome known as Shalaft's Syndrome, then draws a knife and cuts himself. As he passes the knife to Data, Shinzon extends a dinner invitation to Picard.

Back on Enterprise, Dr. Crusher uses the blood from the knife to confirm the captain's suspicious: Shinzon is a clone of Picard. The crew is mystified, however, as to why he exists.

Meanwhile, on Romulus, Shinzon's Romulan supporters are growing impatient — they don't understand what Picard and the Enterprise have to do with his plan. Shinzon merely tells them to have patience, then surreptitiously asks one of the Romulan commanders, Donatra, to keep an eye out for any treacherous action. Later on, Shinzon dines with Picard, and provides an explanation as to how he came to be. Apparently, there was a Romulan plot to replace Picard with a clone, but it was interrupted when Shinzon was only a child. The Romulans then sent him to work in the dilithium mines on Remus. It was there that Shinzon was taken in by one Reman in particular, the man who now serves as his Viceroy. Now, Shinzon says he only wants freedom for his Reman brothers. Picard doesn't quite trust Shinzon yet, but says that he hopes to ? one day. Once Picard has left, the Viceroy reminds Shinzon not to forget their mission.

Back on Enterprise, Picard receives disturbing news. La Forge informs him that unauthorized access to the main computer has been detected. Also, while reviewing the sensor logs, La Forge noticed that when the Scimitar decloaked, the presence of thalaron was detected. Thalaron is a deadly form of radiation that was banned by the Federation — a microscopic amount has the ability to kill all living matter. Disturbed, Picard orders the crew to find a way to stop this deadly threat.

That night, newlyweds Troi and Riker are in bed together. Suddenly, Troi's husband is no longer with her — he has been replaced by Shinzon! Somehow, he and the Viceroy are inside her mind. She manages to summon all of her strength and push him away, but remains shaken. Aboard the Scimitar, the Viceroy tells Shinzon that the bond has been broken. In Sickbay, Troi attempts to explain the attack to Picard and Crusher. Suddenly, Picard disappears and finds himself aboard the Scimitar, with Shinzon. The Picard clone has also transported B-4 to his ship — he was using the android to gain access to Starfleet information. As Shinzon takes a sample of Picard's blood, he explains that his plan is to conquer the Federation, so the Remans may rule the entire galaxy. Shinzon informs Picard that the captain will not be alive to witness this triumph. Once Shinzon leaves, B-4 returns saying that the Praetor needs the prisoner. As they leave, it becomes clear that B-4 is actually Data, who has been feeding the Remans false information. They head for the shuttlebay. After a shoot-out with the Reman crew, they manage to steal a small ship, and head back to Enterprise via the only escape route — through the corridors of the ship. Enterprise beams Picard and Data aboard and jumps to warp.

Meanwhile, the Romulan senate is growing restless — Shinzon has taken no action since coming to power as Praetor. Shinzon once again advises patience. Donatra and the others, however, are beginning to have doubts — they believe Shinzon's plan extends way beyond defeating Earth.

On Enterprise, Dr. Crusher has managed to discover why Shinzon is after Picard. Because of the flawed cloning process used to create Shinzon, his cellular structure is now breaking down. Unless he receives a transfusion from Picard, he will die. Picard deduces that Shinzon will come for him. Meanwhile, Data must deactivate B-4 to prevent the latter from gathering any information for Shinzon.

Later on, La Forge briefs the crew on the Scimitar's thalaron radiation weapon. Given the size and scope of the weapon, Picard deduces that Shinzon must have a particular target in mind — Earth. And there's still no way to penetrate the ship's cloak. The crew prepares for battle, determined that Shinzon will not be allowed to use this weapon, and Enterprise sets off to join the Fleet in Federation space. Data reports that the ship will be "blind" as it passes through the Bassen Rift. Picard orders evasive maneuvers, but it's too late — Enterprise is fired on by the Scimitar, taking out the warp drive. In the midst of battle, Shinzon asks Picard to meet him in the captain's ready room. Picard arrives to find a holographic Shinzon, who orders him to surrender. The captain tries to reach Shinzon, saying that the Praetor has the untapped potential to be a better man. Shinzon, however, says that he cannot fight what he is.

As the battle continues, Enterprise receives some surprise assistance from a pair of Romulan warbirds commanded by Donatra. The Scimitar engages the ships in battle, and Donatra's warbird is soon disabled. At this point, Troi says that she may know of a way to locate the cloaked Scimitar. Using her mental link with the Viceroy, Troi is able to find the ship, and Enterprise manages to bring down the cloak. The Scimitar fires back, and Enterprise loses its shields. A furious Shinzon orders a Reman boarding party to bring him Picard. In response, a security team led by Worf and Riker sets out to stop them.

At this point, only a force field is keeping the Bridge crew from being sucked into space. Determined to stop the Scimitar no matter what the cost, Picard uses all of Enterprise's remaining power to ram the ship. Meanwhile, Riker finds and kills the Reman Viceroy.

The Scimitar begins to pull free, so Picard attempts to destroy Enterprise in a final, desperate maneuver. Auto-destruct, however, is off-line — and the thalaron weapon has begun to deploy. Grimly, Picard decides that there's only one way to stop the weapon — he will beam over to the Scimitar. As soon as he does so, Data orders Troi to take command and heads for one of the damaged ends of Enterprise. La Forge lowers the force field, and Data launches himself out into space, towards the Scimitar.

On the Reman Bridge, Picard has managed to kill much of the crew and is locked in deadly hand-to-hand combat with Shinzon. Finally, he uses a spear-like piece of the ship to impale his clone. Shinzon forces himself along the spear until he is right next to Picard. With his dying breath, Shinzon tells Picard that their destiny is complete. Suddenly, Data appears. The android moves Shinzon's body off of Picard and slaps an emergency transport device on his captain. Before Picard can protest, he has dematerialized. Data fires on the thalaron activation matrix, and the weapon explodes. From the Bridge, Picard and the Enterprise crew watch the explosion in horror, realizing that Data has sacrificed himself.

Later, the senior officers gather to remember their lost friend. Picard also wants to tell B-4 about his courageous brother, but the android still appears not to completely comprehend what has happened. As Picard is about to leave, B-4 softly sings to himself: "Never saw the sun ... Never saw the sun ..." In a moving moment, the captain realizes that B-4 is singing "Blue Skies," the same song that Data serenaded the crew with not so long ago. Perhaps Data's memory will live on after all.