The Enterprise is assisting an astrophysicist, Stubbs, in performing experiments in a binary star system when suddenly, the ship shakes, the shields drop and the Enterprise is sent hurling through space. After regaining control of the ship, the crew is perplexed by the sudden computer malfunctions encountered. Meanwhile, Wesley realizes that two tiny robots he accidentally let loose may be responsible for the mysterious problems the crew is facing.

The Enterprise receives a message from the Sheliak, a race the Federation had not heard from in over 100 years. The Sheliak insist that a world in the Tau Cygna Five system is theirs and demand the immediate removal of humans from that system. The Enterprise does not believe that humans are on that planet due to the fact that the planet has extremely high radiation levels but travels there anyway only to discover a thriving civilization that refuses to evacuate the planet. Data has to convince the people of the planet to leave or be destroyed by the Sheliak.

The Enterprise is sent to investigate an emergency distress call from the Delta Rana system. Upon arrival, the crew discover that all of the inhabitants have been killed except for one couple. An away team beams down to retrieve the survivors in case the aliens that destroyed the planet returned. The survivors refuse to leave the planet stating they can care for themselves. The away team returns to the Enterprise to discuss the situation and are attacked by an alien ship. Meanwhile, Troi is suffering due to some strange music she keeps hearing in her mind.

The Enterprise must undo the damage when a primitive civilization discovers a Federation observation team and concludes that the Starfleet personnel are gods.

A sudden explosion kills Marla Aster on a mission to explore the home of a londead race. Worf, who commanded the away team, rages about the senseless nature of the women's death and plans to offer the Klingon bonding rite to her remaining son, Jeremy. Meanwhile, an energy field is discovered on the planet and Troi senses an alien presence rising upward from it toward the ship. Almost immediately, Jeremy sees his mother who has come, seemingly from the dead, to take him down to the planet.

After discovering a derelict ship in an asteroid belt, the Enterprise is trapped in an energy field that prevents them from leaving. Furthermore, they begin to lose energy reserves and discover that their shields will not keep out the radiation for long. Geordi races against time, with the assistance of an holographic version of one of the ship's designers, to discover a way to escape the deadly trap.

The Enterprise investiages a distress call on a Federation planet with a particularly harsh surface and winds. The away team finds the remains of a Romulan ship and one Romulan, barely alive. The away team beams aboard the Enterprise with the Romulan, accidentally stranding Geordi on the planet where he, moments before beaout time, stumbled into a pit. The crew of the Enterprise struggles to keep the Romulan alive and to locate Geordi on the surface. Meanwhile, on the surface, as Geordi moves closer to the beacon the Enterprise left to guide him, he is taken prisoner by a second Romulan, Bokra. Geordi attempts to convince Bokra that they must work together to stay alive and be rescued while a Romulan Warbird closes in on the Enterprise determined to retrieve their lost comrades from the grip of the Federation.

A race of beings known as the Barzan have discovered the only known stable wormhole and are willing to sell it to the highest bidder. The Enterprise carries several delegates to the site of the wormhole including a hired representative of the Chrysalian people who takes an interest in Troi. Geordi and Data enter the wormhole and discover that it is not truly stable. Meanwhile, Troi discovers that the representative of the Chrysalians, Ral, is part Betazoid and empathic and has been using his ability to gain unfair advantage in the negotiations.

A science outpost is attacked by the Gatherers, a band of Acamarian renegades. Picard talks with Marook, the Sovereign of Acamar Three, who wants to hunt the Gatherers down and destroy them. Picard convinces her to attempt to negotiate first and she and her cook board the Enterprise to travel to a Gatherer outpost to open talks. While there, the leader of the group is killed by a mysterious assassin.

A Romulan scoutship, with a Romulan Warbird in pursuit, hails the Enterprise and requests asylum. After the Enterprise easily chases off the Warbird, they beam aboard the occupant of the scoutship, Setal, who has information about a new Romulan offensive. The Enterprise crew, skeptical about the defector's claims and motives and attempting to get at the truth, travels to Nelvana 3 where there is supposed to be a Romulan base at which a large Romulan fleet will gather to launch an offensive against the Federation.

The Enterprise visist Angosia 3, a planet which has applied for membership in the Federation. While there, a prisoner escapes jail and Prime Minister Narok asks for assistance in recapturing him. The Enterprise succeeds in capturing him, only to find that he is extremely dangerous and not all that Narok has claimed him to be.

Dr. Crusher is kidnapped by terrorists who are demanding independance for their territory. They use an instantaneous teleportation device, which is slowly killing them, and transport aboard the Enterprise in an attempt to destroy it. Meanwhile Crusher attempts to save the terrorists from the tissue degeneration which is killing them.

While on a mission to rescue a planet from its own moon which has fallen out of orbit, the Enterprise is visited once more by the mysterious Q. This time, Q, totally naked, claims he has been kicked out of the Q-Continuum and asks for sanctuary. Q is now mortal and wants guidance from the crew on how to be human, in exchange for his experience and knowledge. While on the Enterprise, Q is attacked by the Calamarians, a race that wants revenge on Q for acts done to them.

Dr. Apgar, a scientist working on Krueger waves, is killed when the station he was working on suddenly explodes moments after Riker talks with him privately. Chief Investigator Krag, arrives on board the Enterprise and demands Riker be turned over to him to face trial for murder. Picard, unwilling to release Riker without a hearing convinces the Chief Investigator to allow the circumstances of the incident be recreated on the holodeck with the help of statements from all parties concerned. Meanwhile, bursts of unknown radiation, able to cause damage to metal, plague the Enterprise.

While investigating a temporal rift, the Enterprise encounters a ghost from its own past the USS Enterprise-C, which travels twenty two years into the future and changes the course of history. With the flow of history changed, Tasha Yar still lives and the Federation is losing a decadelong war with the Klingon Empire.

Data, after returning from a cybernetics conference, builds a robot child, Lal. While the crew attempts to deal with Data's fatherhood, Data attempts to teach Lal about humanity. Starfleet Admiral Haftel, after hearing about the experiment, attempts to convince Picard that the new robot should be moved to the Daystrom Institute where she can be properly studied and taught.

As part of the exchange program that once made Riker First Officer on a Klingon ship, Commander Kurn joins the Enterprise. Kurn is Worf's younger brother and has come to tell Worf that their father has been accused of betraying the Klingons by revealing the location of the Khitomer outpost to the Romulans. Worf, by Klingon tradition must travel to the homeworld of the Klingon empire to challenge the accusation and, if he fails, will die as a traitor.

Picard is taken from the Enterprise while he sleeps by a strange probe and wakens in a prison with two other captives. Neither can explain how they came to be there nor have they seen their captors. Soon they are joined by a fourth captive - a carnivorous alien who will eat the others if they do not escape and food is not provided. In the midst of mutual dislike and lack of trust, the four captives must find a way to escape or contact their captors. Meanwhile, Picard has been replaced on the Enterprise by a nearly exact duplicate.

Picard is talked into taking a vacation on Risa, a pleasure planet. When he arrives, he bumps into a women who, pursued by a Ferengi, grabs him and kisses him as if they were old friends. They later meet again and, after introductions, Picard discovers that she is out to find the location of a device brought from the future. The Ferengi also wants the device or the disk that the woman, Vash, has that reveals the location of the device. Meanwhile, two security agents from the future confront Picard and tell him that he is destined to find the device and they have come back in time to retrieve it from him. Vash and Picard team up to find he device and thwart the Ferengi but, Picard hopes to turn it over to the security agents.

The Hood unexpectedly joins the Enterprise and delivers their new orders and a passenger, Tam Elbrun. Tam is a Betazoid telepath and specializes in first-contacts but, he is also not well liked because he lacks tact. Tam explains that a recently discovered object in orbit around a dying star is suspected of being a living spaceship, dubbed "Tin Man" and Tam's mission is to contact it. However, the Romulans claim that space and are also sending ships to contact the newly discovered alien.

Barclay, a shy and incompetent crewmember, retreats to the holodeck to spend his life in a fantasy world hecreates for himself. When Barclay misses an important meeting, Geordi invades his holodeck creation and discovers The Three Musketeers, in which the characters are based on the crew, including Troi as the Goddess of Empathy and Riker as a fearful knave.

Data is using the shuttles to transfer a large cargo of a special element that cannot be transported when, on the last trip, his shuttle mysteriously explodes. The Enterprise is forced to leave the area to deliver their cargo and are not able to investigate the accident. Meanwhile, Data has not been destroyed but captured by Kavis who is a collector of rare and unique things and Data would be a fine addition to his collection.

Ambassador Sarek comes aboard the Enterprise with his staff and new, human wife, to complete treaty negotiations with the Legarans who insisted on him mediating. Soon after his arrival, the crew of the Enterprise begin to suffer from bouts of violence and other emotional outbursts. Eventually, the crew discovers that Sarek is suffering from a rare Vulcan disease that erodes all emotional control in Vulcans. Since Vulcans are highly telepathic, he has been broadcasting emotions to the crew. But, because of his illness, the important treaty with the Legarans is in jeopardy.

The Enterprise travels to Betazed for a reception following a trade agreement. While there Deanna visits her mother and gets into an argument about settling down and raising a family. Meanwhile, Daimon Tog, of the Ferengi, takes a liking to Lwaxana both sexually and because her telepathy will help him in making deals. Lwaxana is repulsed by his offers and orders him away. Tog, not to be dismissed so easily, kidnaps Lwaxana (along with Riker and Deanna) and takes them aboard his ship where he hopes to convince Lwaxana to marry him.

The Enterprise rescues an injured human from a damaged escape pod in an unexplored system. Dr. Crusher finds that his recuperative powers are incredible and that he will revive, given time. When he does, he has no memories of who he is, where he is from, or how his ship was wrecked. Still suffering from bouts of severe pain, Dr. Crusher finds that he is emitting inixplicable energy bursts which are somehow linked to his cells. Furthermore, he begins to exhibit strange abilities like being able to heal injuries with the energy bursts.

The Borg begin an invasion of Federation space much sooner than was expected. With the Enterprise unable to affect them, the Borg capture Captain Picard and turn him into one of their own.