A Champagne bottle tumbles through space, slowly drifting towards its intended target, the new U.S.S. Enterprise NCC-1701-B. It is late in the 23rd century, and the inauguration of the vessel is attended by crew from the former starship of the same name — James Kirk, Montgomery Scott and Pavel Chekov. Reporters and onlookers clamor to interview Kirk and the new U.S.S. Enterprise captain about commanding a starship, as the crew begins to embark on its routine maiden voyage. A short time into the flight, however, the starship receives a distress call and is diverted to aid two El-Aurian transport vessels which are caught in a strange, mysterious energy ribbon. Kirk, falling back on his old instincts, quickly finds that not only is the new captain inexperienced, but most of the ship's vital weapons and functions have not yet been installed. While Kirk, Scott and Chekov struggle to save the ship, the transporter room beams aboard survivors, even as their El-Aurian transport vessels are torn apart by the energy ribbon.
Kirk goes below deck to work on the deflector relays, but the ribbon suddenly strikes the starship, tearing a large gash through the hull and leaving only debris where Kirk was working. Scotty and Chekov stare out into space, bewildered by the sudden loss of their friend.
Seventy-eight years later, in 2371, the crew of the U.S.S. Enterprise NCC-1701-D join together on the holodeck for a ceremony to promote Lt. Worf — a Klingon officer — to the rank of Lieutenant Commander. The ceremony is conducted using a 19th-century sailing ship and corresponding uniforms. The merriment is suddenly interrupted, however, when Picard receives an urgent personal message. Suddenly depressed, Picard leaves the festivities to contemplate in privacy.
Meanwhile, officers Geordi La Forge and Data successfully install an emotion chip designed by Data's creator, Dr. Noonien Soong, into the android. Although La Forge questions the wisdom of the installation as a potentially painful step in the growth of his friend, Data ignores him. After installing the chip, Data quickly discovers the vast array of emotions now available to him and believes he has the necessary skills to integrate them into his programming.
Sent to the Amargosa Observatory to investigate a distress call, the U.S.S. Enterprise finds two dead Romulans and five humans left alive after a mysterious and brutal attack. One of these survivors is a Dr. Tolian Soran. Data and La Forge later return to the starship's laboratory and find traces of a volatile explosive which Soran has secretly concealed in the lab. While Data watches in abject terror, Soran kidnaps La Forge, taking him to a cloaked Klingon ship. When questioning La Forge proves unsuccessful, Soran releases the starship officer — after modifying his VISOR to transmit its signals back to the Klingon vessel.
Soran then fires a trilithium probe into the sun, which causes an incredible shock wave. The Klingon ship, on which he is a passenger, is commanded by the Klingon Duras sisters. In exchange for the formula for Soran's trilithium explosive, they have agreed to take him to the planet Veridian III, where he wants to conduct another solar implosion.
On board the U.S.S. Enterprise, Picard learns that Soran is 300 years old and, like Guinan, a survivor of the El-Aurian incident that killed Captain Kirk. In an effort to understand what is happening, Picard finally goes to Guinan. She tells him that the energy ribbon, called the Nexus, is a temporal anomaly moving through space. To anyone or anything inside the Nexus, linear time has no meaning and a person can experience anything that he or she desires. There is an overpowering feeling of joy so addictive, that once there, no one wants to leave. Soran is desperate to return to the Nexus and recreate that joy with the family he lost when his world was assimilated by the Borg.
Picard, still depressed from his previous message, informs Troi of his family lineage and that he never intended to have any children because his brother had children who would carry on the Picard name. However, according to the message he received, his brother and nephew were killed in a fire on Earth. Therefore, Jean-Luc will now be the last Picard.
In Stellar Cartography, Picard and an emotionally troubled Data plot the course of the Nexus and the changes that have occurred since the sun was destroyed. They conclude that Soran plans to destroy another sun when the Nexus passes close to the Veridian system — killing as many as 230 million inhabitants on one of the system's planets. Destroying the suns alters spacial forces, thereby changing the path of the Nexus. With the Veridian sun destroyed, the Nexus will then pass along the surface of Veridian III, allowing Soran to re-enter the phenomenon.
Picard, learning of the situation, beams down to Veridian III to try to dissuade Soran. In the meantime, La Forge has been returned to the U.S.S. Enterprise in exchange for Picard; the Duras sisters watch with great interest as La Forge moves about the ship. Finally they see what they've been waiting for — the U.S.S. Enterprise deflector shield modulation. Seizing this information, the cloaked Bird-of-Prey fires through the starship's deflector shields, severely damaging the U.S.S. Enterprise. Ultimately, however, the U.S.S. Enterprise succeeds in destroying the Klingon warbird, killing all aboard. Unfortunately Soran has already beamed down to the planet Veridian III.
Due to damage sustained by the Klingon's attack, the Enterprise suffers a warp-core breach and Riker orders the saucer section separated. Before he can get the saucer away safely, however, the battle section explodes, hurtling the saucer and its entire crew toward the surface of Veridian III. After a terrifying ride, the U.S.S. Enterprise saucer crash lands on the planet's surface. Fortunately, most of the crew are uninjured.
Elsewhere on the planet's surface, Picard and Soran fight to the death as the Nexus rapidly approaches. Soran manages to fire his trilithium probe into the sun, destroying it as the ribbon engulfs both men, taking them inside the Nexus. In their wake, the inhabitants of the Veridian system, as well as the survivors from the U.S.S. Enterprise, are engulfed in a giant cloud of fire.
For a time, Picard is bewildered but delighted to be spending Christmas with his large, happy family — a family he's never had the time to start. But then, just as the captain gazes at a sparkling ornament, he is suddenly reminded that this experience is not real and that he must get on with his mission. Picard remembers that Guinan had told him he would find someone in the Nexus to help him defeat Soran. Just then, an "echo" of Guinan appears, telling Picard that he can have anything he wants in the Nexus, but that he can also leave — and he can leave prior to when he came. There might still be time to stop Soran's destruction, but Picard believes he needs help if he's to be successful.
With Guinan's help, Picard finds a slightly puzzled but happy James T. Kirk in the Nexus. Kirk wasn't killed 78 years earlier on the U.S.S. Enterprise NCC-1701-B, but was drawn into the Nexus instead. Picard meets a content Kirk who is now a happy farmer in Iowa, complete with his life's loves — "Antonia" and his horses. Picard is successful in convincing Kirk of the spurious nature of the Nexus realities, and he awakens Kirk's taste for adventure, duty, and the chance to "make a difference again." The two Enterprise captains leave the Nexus and materialize on Veridian III, just as Soran is preparing to set off his solar bomb. This time, Kirk grapples with Soran while Picard races to sabotages the probe.
Although Kirk wins the fight, knocking Soran off the edge of the cliff, the diabolical doctor manages to cloak the launch mechanism before Picard can disarm it. Yet Soran, hanging on for dear life at the end of a rope, loses control of the remote after the line suddenly gives. The remote control is thrown into the air, landing on a nearby bridge. Kirk races to recover the remote, as does Soran, who fires on Kirk and the bridge with his deadly disruptor. Although Kirk is saved in the nick of time by Picard, the bridge is broken in two, with the remote resting on the opposite portion across the void.
Picard urges Kirk to accept his help, yet Kirk, stubborn as always, goes after the remote himself. With the second half of the bridge about to give, Kirk jumps to the other side, escaping certain death by seconds. Just as the remote is about to fall into the chasm, Kirk miraculously grabs it out of thin air. With time running out and the Nexus fast approaching, Kirk decloaks the launch mechanism. Suddenly the second half of the bridge collapses into the chasm, carrying Kirk with it.
Picard, now able to see the mechanism, races to the controls. Yet his plans are seemingly cut short when Soran, frantic that he might miss his last chance at gaining access to the Nexus, aims his disruptor directly at the captain. Although Picard escapes, capitalizing on Soran's distraction, the evil doctor doesn't care. His moment of triumph is at hand. Soran's smile slowly fades, however, when he realizes that Picard has secured the missile's locking clamps; although about to ignite, the rocket will not launch.
The launch mechanism explodes into a giant fireball, killing Soran and preventing the destruction of the entire Veridian system. Picard runs to Kirk, where he stays until the former captain of the U.S.S. Enterprise dies. "It was fun...oh my." are Kirk's last words. After Picard has buried and mourned the loss of his new friend, a shuttlecraft from the U.S.S. Enterprise finds Picard and takes him to the ship's crash site where survivors are being rescued by the U.S.S. Farragut.
Believing he has finally mastered human emotions, Data finds himself wrong when he and Counselor Troi manage to find the android's cat amongst the Enterprise wreckage. Data, bewildered, is overcome with tears of joy. Riker is saddened as they leave the wrecked starship, but Picard assures him that this is not likely to be the last ship named "Enterprise."