At the close of last season, Captain Picard had been captured. As the new season begins, his captors have mutilated him into a half-Borg, half-human called Locutus, and have been manipulating him to gain insight into human behavior to aid their plan to conquer Earth and enslave humanity. They have also accessed Picard's extensive knowledge of the U.S.S. Enterprise, its crew, and their strategy to defend Earth. In Picard's absence, Fleet Admiral Hanson promotes First Officer Riker to captain. Riker finds the adjustment painful and difficult, but eventually takes the captain's chair and names Lieutenant Commander Shelby as his First Officer despite their initially hostile relationship. The new captain then commands his ship toward a rendezvous with Starfleet. En route, the crew is horrified by the discovery of a literal graveyard of Starfleet ships, left behind as a grim sign of the Borg's path of destruction toward Earth. Learning of their intentions to assimilate the culture and technology of the U.S.S. Enterprise through Picard/Locutus, Riker realizes he can use his former captain to foil the Borg. He searches for a way to use Picard/Locutus to access Borg information in the same way the Borg tapped the captain for U.S.S. Enterprise secrets.
After taking the U.S.S. Enterprise to an Earth orbiting spacedock for repairs, Picard, still recovering from the injuries he suffered at the hands of the Borg, returns for the first time in twenty years to the 19th century French village where he grew up. He is greeted warmly by his sister-in-law and nephew, both of whom he has never met. However, his meeting with his older brother Robert, who feels that Picard is arrogant, is filled with animosity. Back on board the U.S.S. Enterprise, Worf receives an unexpected visit from his adoptive human parents, Sergey and Helena Rozhenko. Because he is a Klingon, Worf is uncomfortable with their displays of emotion. His coldness upsets Worf's mother. But her feelings of hurt and helplessness are alleviated after a conversation with Guinan, who assures the Rozhenkos that when their son looks toward home, he is looking toward Earth. Comforted by her words, the couple assures Worf that while they may not understand everything about his association with the Klingons, they will always stand by him and love him.
Aboard the U.S.S. Enterprise, a young boy's practical joke backfires and leaves his brother dangerously ill. Because the boy needs special treatment to survive, the ship rushes towards a nearby Starbase. En route, Data begins to inexplicably malfunction, slipping into a trance-like state and altering the ship's course. He then severs the life support system on the Bridge, forcing the evacuation of the command crew, and leaving himself alone on the Bridge. He thwarts the crew's numerous efforts to regain control of the ship by speaking to the computer in Picard's voice and taking control of the U.S.S. Enterprise. The starship continues to follow his mysterious course, while the sick little boy's situation grows more desperate.
Responding to a distress call from a stricken Talarian vessel, an Away Team from the U.S.S. Enterprise discovers that the ship is manned by five teenagers -- one of whom is human. While treating them, Dr. Crusher finds that the young human shows signs of severe abuse. The boy, called Jono, will not communicate with anyone among the crew, and responds to Picard only upon learning that he is a captain. The boy requests that Picard return him to Endar, the Talarian father who raised him. Fearing for the boy's safety, Picard refuses. Starfleet reveals that Jono is actually Jeremiah Rossa, an orphaned human member of a Federation outpost presumed dead in a battle ten years before. His human grandmother, a Starfleet admiral, is anxious for his return, but Troi fears readjusting to the human lifestyle could be traumatic for him. When Picard asks Troi to work with the boy, she reminds him that since Talarians respond only to male authority, he must be the one to help Jono.
After escorting her friend Dr. Dalen Quaice aboard the U.S.S. Enterprise, Beverly is deeply moved by his sadness over losing his wife and other people he has loved. She seeks out her son Wesley, and finds him in engineering, working with a warp bubble on a computer screen. While she watches, his experiment inadvertently causes a strange flash of light. Soon afterward, Dr. Crusher is unable to locate Dr. Quaice. The ship's computer reports that he has never been on board, and Picard and Worf inform her that they had no knowledge of his presence on the ship. Additionally, O'Brien does not recall transporting Quaice aboard, and Starfleet has no record of the doctor's existence. Beverly's bewilderment turns to concern when members of the crew, including her entire medical staff, begin to disappear. Neither their relatives, other crew members, or the ship's computer remember their ever having existed.
The crew responds to a distress call from a stricken Federation freighter that is orbiting the planet Turkana IV, birthplace of their late comrade, Tasha Yar. The freighter explodes, but Data detects an escape pod heading toward the planet. Picard dispatches an Away Team to rescue the crashed crew members. Upon reaching the planet's surface, Riker and his team meet Hayne, leader of the Coalition - one of the planet's two warring factions. When Data reveals that a former crewmember was born on Turkana IV, Hayne offers to aid in the search with the help of one of his comrades, Ishara Yar -- Tasha's sister.
K'Ehleyr, a half-human, half-Klingon ambassador, requests permission to come aboard the U.S.S. Enterprise to speak with Picard. Worf is noticeably agitated when the woman, his former mate, materializes accompanied by a young Klingon boy. K'Ehleyr tells Worf that the boy, Alexander, is their son. The Ambassador then informs Picard that she has come because K'Mpec, the dying Klingon leader, wishes to speak with him. Picard boards the Klingon ship, and K'Mpec requests his help in arbitrating the power struggle between his two potential successors. One of the contestants has been secretly poisoning him, and Picard must determine who is the murderer and prevent him from assuming K'Mpec's post.
When Data receives strange energy readings from Alfa Onias III, an uninhabited planet near the Neutral Zone, Picard suspects the Romulans and sends an Away Team led by Riker to investigate. On Alfa Onias III, communications with the Enterprise break down and the mission is aborted. Later, Riker awakens in sickbay to a graying Dr. Crusher, who tells him that he is recovering from a retroactive virus he contracted during the mission sixteen years ago -- a virus that only recently became active and destroyed all of his memory from the moment he was infected. Riker learns that he has been Captain of the U.S.S. Enterprise for nine years, but his most shocking discovery is that he is about to lead negotiations for a peace treaty between the Federation and their long-time adversaries, the Romulans.
Picard summons Wesley to the Bridge, where he informs the youngster that he has been accepted to Starfleet Academy. He further honors Wesley by asking him to accompany him on a final mission to help mediate a dispute on Pentarus V. When the U.S.S. Enterprise is called to investigate another nearby crisis, Picard and Wesley proceed alone, traveling with a representative of the planet, Dirgo, in his dilapidated shuttle. En route, the shuttle fails, forcing an emergency landing on a desert-like moon. Upon learning Dirgo is not traveling with water, Picard positions a makeshift arrow in the sand to indicate their direction and heads toward a mountain range for shelter.
When starship sensors detect a strange pattern of images in the U.S.S. Enterprise's path, the crew stops to investigate. Unable to pinpoint the source, they attempt to resume their course, to the shocking realization that they are being pulled by an unknown force -- a force they are unable to break away from. Worried, Picard calls an emergency staff meeting and asks Troi if she senses a life form. The counselor suddenly realizes that she is unable to sense anything from the force or from anyone else in the room. Her empathetic powers have failed.
Data is excited about his friend Keiko's upcoming wedding to Chief O'Brien, where the android will be giving the bride away. When the bride succumbs to jitters and calls the wedding off, Data applies android logic, and decides that since O'Brien loves Keiko, if calling off the wedding makes her happy it will make O'Brien happy. Of course, the heartbroken groom's reaction to Data's news quickly reflects otherwise. Data's confusion is compounded when Geordi assures him that the wedding will proceed as planned. With this in mind, he attempts to buy a gift for the couple, and encounters Worf, who informs Data that he will have to dance an the wedding. Data has never danced, so he enlists Dr. Crusher's help -- after learning from her file that she was once a tap dancing champion.
After a Cardassian warship fires on the U.S.S. Enterprise, the ship's captain informs Picard that he is acting in retaliation against a Federation starship that has recently destroyed an unarmed Cardassian space station. This is unusual because there is now a treaty between the Federation and the Cardassians, who were once bitter enemies. As a goodwill gesture, Picard invites the Cardassian captain aboard to aid in the search for the renegade Federation vessel, despite the objections of some crew members who still mistrust their former enemy. Starfleet informs Picard that the errant Federation ship is the U.S.S. Phoenix, commanded by Captain Benjamin Maxwell.
The U.S.S. Enterprise receives an emergency transmission from a science station on the planet Ventax. The Ventaxians are in a panic, convinced a mythic figure called Ardra has returned to fulfill a thousand-year-old contract. According to legend, she promised the citizens of the once war-torn planet a thousand years of peace and prosperity in exchange for their enslavement at the end of that time. When Picard takes Worf, Data and Troi to the planet to help Jared, the Ventaxian leader, Ardra suddenly appears before them.
En route to investigate a mysterious planet, the U.S.S. Enterprise passes through a 'worm hole' in space which knocks everyone but Data unconscious. As the crew begins to revive, Data tells Picard that they were out for 30 seconds, and when Riker remarks that the ship's instruments indicate an entire day's travel, Picard blames the discrepancy on the wormhole. Data talks Riker and Picard out of going back to investigate the planet, sending a probe instead. When the probe reaches the planet, its reading conflicts with the crew's original assessment. Data blames this on the wormhole as well. Geordi soon discovers that the ship's chronometer, which only he and Data have the power to reset, has been tampered with. Unable to ignore the fact that something is causing Data to lie, Picard orders the android to undergo an examination.
During a mission on a strange planet, Riker is wounded and stranded in a hospital without his communicator. While he is unconscious, his Malcorian doctors discover evidence that proves he is not of their race. When he comes to, Riker refers to himself by a Malcorian name and passes off his physical differences as deformities. His doctors, however, believe he is an alien, and decide to keep his presence a secret to avoid a panic among their people. Meanwhile, Picard and Troi surprise Mirasta, the Malcorian Minister of Science, when they materialize in her office.
When Captain Picard asks Geordi to escort a visitor, Dr. Leah Brahms, aboard the U.S.S. Enterprise, Geordi is thrilled. He confides to Guinan that Leah, the woman who designed the U.S.S. Enterprise's engine, is the woman of his dreams. During a crisis, he recreated a Holodeck image of Dr. Brahms to help him and felt a strong rapport with her. But when the real Leah finally transports aboard, he is crushed to discover that she is cold, cerebral and humorless. She puts him through his paces, icily examining and criticizing the adjustments he has made to the engine she helped design. Meanwhile, Picard and the crew discover a large energy source floating in space. When they approach the creature to learn its origin, it suddenly latches onto the starship, bombarding the ship with deadly radiation. In defense, Picard fires the ship's phasers to release the U.S.S. Enterprise from the alien's clutches. Picard is saddened when the phaser assault kills the lifeform, but he is intrigued when Data detects another energy reading within it. To everyone's surprise, Data explains that they have discovered a 'baby' struggling to escape its dead mother's womb.
The U.S.S. Enterprise locates the Brattain, a science vessel which has been adrift for several days, only to discover that the entire crew, with the exception of the ship's Betazoid counselor, is dead. Troi tries to communicate with the survivor, but can deduce no information that unsheathes the mystery that took place onboard the frigate. After performing autopsies on the crew members, Dr. Crusher concludes that the 34 men and women killed each other. As Troi is being tormented by strange nightmares, Geordi finds that while there is nothing wrong with the Brattain's engines, he is unable to activate them. While Geordi tries to rig the Brattain to the U.S.S. Enterprise to be towed, members of the crew begin exhibiting signs of increased irritability and paranoia. Troi and Beverly approach Picard to warn him that whatever happened aboard the Brattain may be starting aboard the U.S.S. Enterprise, and recommend leaving the area as soon as possible. Picard agrees, but when they try to leave, the engines shut down -- just as they had on the Brattain.
Geordi's friend and former shipmate, Susanna Leijten, informs him that the two of them are the only crew members remaining from an Away Team that once investigated the mysterious disappearance of several people on the planet Tarchannen. The last of their former colleagues has stolen a shuttlecraft to head back to the planet, and Susanna enlists the U.S.S. Enterprise's aid to find out what is happening. The starship follows the shuttlecraft to the planet discovering two additional shuttlecrafts on the surface, but no life signs. After Geordi finds two torn Starfleet uniforms, Susanna tells him she senses the presence of the others and heads off into the darkness. When Geordi tries to stop her, she begins thrashing like a wild animal. He has her beamed to Sickbay.
When the U.S.S. Enterprise sets out to repair the Argus Array, a telescope that has stopped relaying data for two months, the crew discovers an alien probe near the telescope. Geordi takes Barclay, a notoriously shy crew member, to investigate. As they near the probe, it emits an energy surge that knocks Barclay unconscious, and he and Geordi are transported to Sickbay. Meanwhile, the probe begins to follow the Starship, emitting a dangerously high energy level. When the crew is unable to evade it, Barclay amazes everyone by taking charge of the situation and eliminating the probe, saving the ship from destruction.
When the U.S.S. Enterprise hosts an archaeology symposium, Picard rekindles a romance with Vash, an archaeologist he met while on vacation. The obvious passion between the two is strained, however, when Vash learns that Picard has never mentioned her to his friends, and he discovers that she plans to make a secret excursion to a planet that is closed to outsiders. The omnipotent, immortal ester Q secretly witnesses a heated argument between the two. After Vash leaves, he appears to a shocked Picard and tries to elicit a confession of love from the stoic Captain. Picard refuses, and Q responds by transforming the Captain into Robin Hood and sending him to Sherwood Forest, where he is joined by his senior staff, who are now merry men. Q dons the disguise of the Sheriff of Nottingham, and tells Picard that Vash, who is now Maid Marian, will be beheaded the following day - challenging Picard to risk the lives of his crew to rescue a woman he claims he does not care about. Picard claims he would do the same for anyone in danger and sets out to rescue Vash, but orders the others to stay behind.
When an explosion rips through the U.S.S. Enterprise's warp engine, a visiting Klingon officer is suspected of causing the disaster by providing the Romulans with schematics of the engine. An investigation begins, and Admiral Norah Satie, renowned for exposing an alien conspiracy against Starfleet, comes out of retirement to help. Based on evidence compiled by Worf, Satie quickly extracts a confession from the Klingon, J'Ddan, regarding his participation in smuggling diagrams off the ship, but he denies responsibility for the explosion. Satie's Betazoid aid Sabin confirms that J'Ddan is telling the truth, which implies to Satie that there is a coconspirator aboard the ship.
While a passenger aboard the U.S.S. Enterprise, Troi's overly-amorous mother Lwaxana becomes infatuated with Dr. Timicin of the planet Kaelon Two. The rather reserved Timicin, a leading scientist who has enlisted the Federation's aid in saving his planet, is equally smitten with Lwaxana, and the two begin spending time together. Timicin has boarded the Starship Enterprise to test an experiment that he hopes will revitalize the dying sun of Kaelon Two. The U.S.S. Enterprise assists him by transporting him to a similar sun in a remote region of the galaxy where the scientist can test his theories. With the help of the crew, Timicin fires photon torpedoes into the surrogate sun in an effort to elevate and stabilize the temperature. At first, the experiment seems successful, but the sun's temperature continues to rise to dangerous levels, forcing the starship to evacuate the region and return to Kaelon Two. Later, when even the charming Lwaxana is unable to comfort the defeated Timicin, he confides to her that he is returning home to die.
Beverly becomes romantically involved with a Trillian ambassador who is being escorted by the U.S.S. Enterprise to mediate a dispute in the Peliar system. As the starship approaches its destination, Riker volunteers to shuffle the ambassador, Odan, to Peliar to meet with representatives of the planet's Alpha and Beta moons, which have armed for war against each other. Shortly after Riker and Odan depart, a ship opens fire on them, critically injuring Odan and forcing their return to the U.S.S. Enterprise. Back on board, Beverly's examination of Odan indicates that a parasite is invading his body. As she prepares to remove it, she is shocked when Odan stops her, revealing that he is the parasite, and his body is merely a host. The parasite, not the body, is what must be saved.
En route to a vacation and seminar on Risa, Geordi is kidnapped by the Romulans and subjected to days of brainwashing. While a double is sent to replace him at the conference, Geordi is forced to endure a painful series of mind-altering experiences designed to put him under complete Romulan control. Meanwhile, the U.S.S. Enterprise is assigned to escort Klingon Ambassador Kell to the Kriosian System, where one of the Klingon colonies is fighting for independence. The governor of Krios, Vagh, charges that the Federation is secretly aiding the rebels. Though Picard denies the accusation, Vagh produces weapons seized from the rebels which appear to be Federation issue.
Ensign Jenna Anaya, 'on the rebound' after breaking up with her boyfriend, suddenly begins relating to her friend Data as something more than a friend. After the young woman kisses him passionately on the lips, the confused android asks his friends for advice on what to do, and decides to pursue the relationship. Since he has no real emotions or feelings, Data creates a special program to guide him through the intricacies of love. However, as his relationship with Jenna progresses, he discovers that in romance, the logical course is not always the most appropriate. With this in mind, he picks a fight with Jenna, later explaining that he did it because his study of interpersonal dynamics suggested that conflict often strengthens the bond between two people. When Jenna points out that there is something artificial about his behavior, he concurs, reminding her that all of his behavior is based on a program and is therefore artificial.
The U.S.S. Enterprise travels to the Klingon Empire, where Picard is to attend the installation of Gowron, the new Leader of the High Council. En route, the starship is intercepted by a Klingon ship bearing Gowron, who informs Picard that the Duras family is amassing a rebel faction and plotting civil war against the Empire. Duras, the slain challenger for leadership of the High Council, was responsible for Worf's discommendation and was also found guilty of conspiring with the Romulans. Based on the discommendation, Gowron asks Picard to ban the Duras family from the Council, but Picard insists that such action is beyond his jurisdiction.