In this conclusion to the cliffhanger finale of the sixth season, Troi, Picard, and Geordi are captured by the Borg and Data's brother Lore who is the leader of this group of renegade Borg. Lore plans, with Data's help to create a new race of beings to become masters of the universe. Meanwhile, Riker, Worf and most of the crew of the Enterprise follow Picard down to the planet to try and locate the missing members of the away team leaving Dr. Crusher in command of the Enterprise.
An Iyaaran delegation visits the Enterprise for the first formal diplomatic function between Iyar and the Federation. Picard is scheduled to shuttle back to Iyar, while Iyaaran ambassadors Loquel and Byleth remain on the Enterprise. The Iyaaran shuttle taking Picard back to their homeworld crash-lands on a planet covered with violent electrical storms, one of whose plasma lightning bolts injures Picard when he leaves the shuttle to look for medical aid for the critically injured pilot. A woman named Anna, who has apparently been stranded alone on the planet for seven years, gets Picard to shelter inside a crashed freighter. On the Enterprise, ambassadors Loquel and Byleth test the patience of their respective hosts, Troi and Worf, while Picard has to contend with a woman whose isolation has driven her to try to keep him in the crashed vessel with her - but Picard learns that no survivors of the freighter's complement or crew are actually still alive.
A new interface is being tested by Geordi to control remote unmanned probes. Utilizing his VISOR implants, Geordi is able to see, hear and experience whatever conditions the probe encounters. His interface with the probe comes in useful while the Enterprise investigates the loss of the starship Raman. But during the mission, Picard receives word that the starship Hera, commanded by Geordi's mother, has disappeared with all hands, and Starfleet, despite dispatching two more vessels to search, does not expect to find the Hera or any of her crew. Geordi is profoundly affected by the news, and when he encounters an image of his mother on the Raman, he goes against his father's advice and Picard's direct orders and tries to use his unique interface with the probe to find out what has happened to her.
Riker, Troi, Worf and Crusher are searching for the missing Captain Picard on Desica II to no avail. A Yridian claims he witnessed Picard's death in a seedy bar after an argument with a group of aliens, and offers to give Riker some clues in exchange for safe passage off the planet. Once aboard the Enterprise, the Yridian leads Riker to a planet in the Barada system, where an away team led by Riker beams down to hunt for possible leads in the investigation. A well-armed group of aliens under the command of a Romulan ambushes the away team, and Riker is captured and beamed away with the attackers. Data takes command of the Enterprise and pursues the alien ship. Riker finds himself in the hands of a band of mercenaries commanded by Baran, a vicious-tempered leader who maintains the loyalty of his crew - and Riker - by using pain-generating implants which he controls. Riker is astounded to find that the newest member of the rogue crew on their mysterious mission to raid ancient Romulan artifacts is a knowledgeable rogue named 'Galen' - better known to Riker as Captain Picard.
Riker is accepted into Baran's outlaw fold by pretending to be an old enemy of 'Galen', and the mercenaries' mission continues. Picard discovers that Baran's gang is not looking for Romulan artifacts, but for ancient Vulcan artifacts. The Romulan mercenary Tallera reveals herself as an undercover Vulcan security operative, and she earns Picard's trust enough for him to reveal his own identity. A Klingon shuttle pilot carrying the last of three vital artifacts is intercepted by the Enterprise, which becomes Baran's next target. Riker is left for dead on the Enterprise by Picard to resume command, as Picard leads a mutiny among the mercenaries and kills Baran. Picard must try to play into Riker's hands without arousing the mercenaries' suspicions - or Tallera's.
Having just received a new warp core from a starbase, the Enterprise departs with both Picard and Geordi ready to test the more efficient drive system en route to an admirals' banquet which Picard is not looking forward to. The warp core fails to perform to expectations - in fact, it fails to perform at all. Simultaneously, Data experiences his first nightmare, and then his second, and his third, all full of disturbing imagery he feels he should not ignore. His friends don't think it's anything to worry about, until Data's nightmare visions drive him to commit acts of violence.
Lwaxana Troi visits the Enterprise again along with a small delegation of Icarans, who communicate in telepathic imagery with no verbal elements whatsoever. To prepare them for their first meeting with the Federation council, Mrs. Troi is trying to help the Icarans learn to translate their imagery into speech, a facility they were born without. Not long after Deanna notices her mother experiencing brief episodes of intense anguish, Lwaxana collapses into a coma, and the only clues to her condition and the reason for it are held by the Icarans, who are not able to fully communicate it.
The world inhabited by the Kes and the Prit is divided; the Prit are xenophobic to the point of hostility, but the Kes have applied for membership in the Federation, which is surprising since they are paranoid to the point of operating like a police state. Beaming down to meet with Kes representatives, Picard and Beverly are kidnapped by the Prit, who believe the potential Kes affiliation with the Federation to be a military pact. Fitted with neural implants to allow their captors to retrieve information without an interrogation, Picard and Beverly manage to escape with the aid of an undercover Kes agent onto the surface, where they are to head to the Kes border. An unusual side-effect of their implants allows them to hear each other's thoughts en route. In the meantime, Riker is trying to glean information about his captain's whereabouts from a Kes representative who is deliberately being less than helpful.
Investigating the mystery of missing starships, the Enterprise finds that a brother and sister have been misleading and damaging all warp-capable vessels that enter the region of space near their home world, claiming that warp engines are agitating a sensitive subspace rift which threatens to destroy everything nearby if it becomes active. Reluctant to accept this theory, Picard and the crew plan to rescue the damaged ships and move along, but when one of the protesters opens the subspace rift with a burst of warp energy, the Enterprise may be unable to escape.
On a mission to salvage an endangered planet, the Enterprise is visited by Dr. Tainer and her husband, two scientists whose plan may save the planet. The first chance she has to speak to Data privately, Tainer reveals herself to be the ex-wife of Dr. Soong and co-designer of Data and Lore. Though he is skeptical at first, Data finds evidence that she may be who she claims to be, and begins to spend time with her in an effort to find out about his creation and development.
Returning triumphant from a Klingon martial arts competition, Worf walks right into a surprise birthday party, but notices that something is amiss aboard the Enterprise; events begin contradicting themselves, and cause no longer leads to a logical effect. His environment and his comrades change - Troi suddenly believes she is Worf's wife; Geordi is killed in engineering during a Cardassian assault. Worf alerts Data to the strange occurrences, and Data begins to research a way to send Worf back to his original universe. Further disparities appear, including Riker's command since Captain Picard's death in the Borg invasion several years ago, and Worf's two children (neither of them Alexander) by Troi. Data discovers the way to send Worf back...but when Enterprises from every possible variation of every potential reality appear, not every crew wants reality restored to its normal flow.
The Enterprise is assigned to head for an asteroid belt in a sensitive area between Romulan and Federation space, with Admiral Pressman from Starfleet Security aboard. Along the way, it is clear that the Enterprise's objective is top secret, and that Pressman and Commander Riker have some old business to discuss. On his first Starfleet mission as an ensign, Riker served aboard the USS Pegasus and witnessed a shipwide mutiny against that ship's captain - Pressman. Riker defended Pressman at the time and they were among a handful of survivors who escaped before the ship was apparently destroyed by a mishap in engineering. Now, twelve years later, Pressman reveals to Riker that the Enterprise's secret mission is to search for the Pegasus - Riker's first starship still eVIsts, and still harbors the treacherous secret that once sparked a vicious mutiny whose nature is still a dark, closely-guarded secret in the files of Starfleet Security.
Dr. Nikolai Rozhenko, Worf's human foster brother, has sent a distress call from his hidden cultural observation post on Boral II, a planet whose atmosphere is going to break down in less than two days. Worf beams down, disguised as a Boralan, only to find that his brother has also been masquerading as a native and providing them with means of survival based on the technology of his observation post. Nikolai is admonished by Picard for his severe violation of the Prime Directive, but when the planet is within seconds of dying, commits an even greater breach by transporting a handful of Boralans into a holodeck simulation of the shelter on their world. The Enterprise crew - especially Worf - are now left with the dilemma of relocatintg the simplistic Boralans to a new world without revealing the true nature of their surroundings. Damage to the holodeck jeopardizes the mission.
The Enterprise is visiting Caldos, a terraformed Earth colony modeled after 17th century Scotland, so Dr. Crusher may attend the funeral of her grandmother. Also attending the funeral is an unknown man whose appearance mystifies Crusher. While the Enterprise crew gives the colony's seismic and meteorological control systems a routine check, strange things begin happening. In her grandmother's journals, Beverly learns that her grandmother, despite being over a century old, had a young lover. When a strange voice appears to her first in dreams and then in waking, Beverly realizes that the mystery man from the funeral - and from her grandmother's past - has come for her as well.
A promotion is nearing for one of a group of four friends who are junior officers aboard the Enterprise. Sito, a Bajoran ensign who was involved in the Nova Squadron accident cover-up at Starfleet Academy with Wesley Crusher, is neck-in-neck for a promotion to Ops with the ambitious Lavelle, who is attempting to make a favorable impression on Commander Riker. Vulcan Ensign Taurik is an engineering specialist whose duties of late have grown mysterious, as have those of Nurse Ogawa, who is also due for a promotion. The Enterprise is undertaking a top secret mission, the true purpose of which is unknown to the four friends - though each of them has a piece of the puzzle, and a part to play, in this critical event.
Counselor Troi returns from her Academy class reunion to find Dr. Crusher in charge of the bridge, and begins wondering about the possibility of achieving her own position in the ship's chain of command. Crusher, for her part, is on watch while Data is away in a shuttlecraft retrieving radioactive fragments of a destroyed space probe. Data's shuttle crashes on a world inhabited by relatively primitive humanoids, and his radioactive cargo disrupts his ability to access his memory of who he is or where he is from. Data wanders into the nearest village carrying the case of hazardous materials, with which he unwittingly contaminates everyone. The only hope for the locals is for Data to restore his memory.
Studying an ancient comet at close range, the crew of the Enterprise becomes aware of strange objects appearing on board. An unexplained surge of energy affects the ship's computer systems and Data as well. The comet is revealed to be an archaic spaceborne artifact of a bygone alien civilization. The Enterprise's computer is filled with symbols and hieroglyphics whose meanings are known only to Data, though he has never before encountered anything like them. Soon, Data himself is transformed, exhibiting a number of personalities from the alien archive. The ship's computer and even parts of the ship itself transform themselves into objects whose function can only be deduced by studying the alien civilization. But by the time Picard and the others can gain an understanding of what has taken control of their ship, the Enterprise and Data will be transformed into an ancient alien temple - and its resident goddess.
A young officer recently posted to the Enterprise commits suicide by leaping into an energy stream in one of the ship's warp nacelles. Trying to find out why, Troi begins investigating the last days of the deceased by speaking to his friends and co-workers, and eventually winds up surveying the warp nacelle post, where she experiences an inexplicable emotional upheaval which may be an echo left by the partially empathic officer's final burst of feelings and thoughts. She tries to probe this psionic artifact for its true meaning, and uncovers a betrayal which is older than anyone realizes.
A routine test of Worf's new photon torpedo guidance system sends a potentially hazardous torpedo astray into deep space, which Picard and Data set off to recover via shuttlecraft. When they return from their mission, they find that every inhabitant of the ship has somehow mutated into more primitive forms of life, some dangerous, others not. The cause of this condition is a virus which has now infected Picard, leaving him and Data very little time to reverse the plight of the crew.
Wesley Crusher, on a sabattical from Starfleet Academy, has returned to the Enterprise in an attempt to recoup his energies in time to graduate. He is troubled by something which he has yet to reveal to anyone, but more pressing matters are on the mind of Picard and the crew as Starfleet orders the Enterprise to evacuate or otherwise remove a colony of Native American Indians who have settled on an isolated planet to preserve their culture. This planet is now due to be handed over to the Cardassians according to the terms of a treaty which realigns the borders of Federation and Cardassian space, and the Indian colonists will no longer be welcome. Tired of their history of being displaced by territorial bureaucracy, the Indians of Dorvin V decide to reshape the borders themselves to protect what they hold sacred - and they find a sympathizer in Wesley, who jeopardizes his Starfleet career to help them and learn more about them.
As Alexander nears the age where he must decide whether or not to become a warrior, Worf grows worried that the boy will choose to shed all vestiges of Klingon heritage. Visiting a Klingon outpost during a festival, Worf and Alexander are cornered by a gang of street thugs. As Worf manages to fight most of them off, the fight is ended by a Klingon who calls himself K'mtar, a bodyguard appointed by Worf's brother Kurn. K'mtar reveals that the attack was not random, but an assassination attempt planned by Lursa and B'etor, who are still scheming to someday overthrow the Empire. With the help of K'mtar, and some gossip courtesy of Quark, the Enterprise is off to track down the Duras sisters when it becomes evident that someone is trying to tamper with future affairs.
Picard learns that he has a son, and that the young man has been targeted for murder by an old enemy in search of revenge. Picard receives a disturbing message from Daimon Bok, the Ferengi whose son Picard killed in battle years before. Bok says he plans to avenge that death by killing Picard's son, Jason Vigo. Picard is unaware he had a son, but did have a relationship with Vigo's mother twenty-four years earlier. Since Jason is in danger regardless of his parentage, Picard sets course for Camor Five, where the young man lives, locates and beams the surprised young man aboard. He is even more surprised when Picard fills him in on the situation, and agrees to take a genetic test, which soon reveals that Picard is Jason's father.
While rehearsing a scene from 'The Tempest' in the holodeck, Data and Picard are amazed when they are nearly run over by the Orient Express, the famed 19th century locomotive whose itinerary never once included Prospero's island. Investigation of this quirk is postponed by the Enterprise's sudden jump to warp speed, and a fortuitous exit from warp just in time to avoid the ship's destruction. When the crew concentrates the search to this problem, a strange modification of the ship's circuitry is discovered, one which seems to be tying many disparate systems together. When the ship's systems take measures to protect the growing anomaly, the truth becomes clear - this is no accident, but a new intelligence all its own taking form within the Enterprise's hull.
A reception for recent Stafleet Advanced Tactical Training graduate Ro Laren is cut short when the Enterprise responds to a Cardassian ship's distress call. Arriving on the scene, Picard and the crew discover that the Cardassians are under attack by a flotilla of small vessels commanded by the renegade Maquis. After chasing them off and assisting the Cardassians, the Enterprise receives a visit from Admiral Nechayev, who delivers to Picard the message that Starfleet intends to use Ro to infiltrate the Maquis, and she accepts the mission, posing as an ex-Starfleet defector and gaining the acceptance of the Maquis. However, when Ro and her 'fellow' Maquis are the targets of a vicious Cardassian sneak attack, she begins to question Starfleet's rationale for stopping the Maquis.
Picard is beginning to jump backwards and forwards through time. He moves to three different time periods. The 'present', a time just before the pilot and a time 25 years in the future. He tries to persuade the crew in the 'present' that he was not dreaming, but there is no evidence of a temporal shift so they did not quite believe him. In the past, the spacial anomaly is in the Neutral zone and Crusher scans Picard and realises that he has accumulated more memories than he should have. They then realise that each time period is operating independantly from each other. In the future, Q then appears and informs Picard that he is responsible for Picard's time shifting and that the Q have decided to terminate humanity and that Picard will be responsible for the destruction of humanity.
In the future, Beverly's ship, the USS Pasteur is attacked by the Klingons but help arrives from the Enterprise commanded by Admiral Riker. In the past and 'present,' people's old scars and wounds begin healing themselves and Geordi's eyes begin regenerating. Q shows Picard the beginnings of life on earth. The anomaly is so large by this time that its time disruptions prevent life from forming on Earth. Picard realises that he must have created the anomaly somehow and that stopped life on earth from forming.