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.....