Stardate: 46001.3 - The away team's investigations are hampered by a nosy Samuel Clemens. Picard discovers that he originally met Guinan in the 1890s on Earth.

Stardate: 46041.1 When trying to rescue survivors from another trapped Starship, Barclay has a terrifying transporter experience. However, this terrifying experience may lead to the rescue of the others of the Starship's crew.

Stardate: 46071.6 The Enterprise comes to the rescue of another Federation ship, which carries a unique Lumerian ambassador and his elder female assistant, who are traveling to mediate a dispute in the Rekag-Seronia system. The Lumerian's assistant takes an immediate dislike to Troi, but then soon dies. Strangely, Troi soon becomes attached to the Lumerian, and also shows signs of beginning to rapidly age.

The Enterprise receives a distress signal from a 75 year old Federation vessel, and discovers it has crashed on a Dyson Sphere, an enormous structure where a shell is artificially created which surrounds a star at roughly the same distance as the earth is from the sun. Investigation of the crashed transport finds that one of the ship's passengers has actually survived the intervening time looped inside the ship's teleporter, and it turns out to be an old friend of the Enterprise...

Stardate: 46154.2 - Members of the crew are secretly abducted from the Enterprise to be used in bizarre experiments where they are dismembered and re-assembled without anyone's knowledge - including their own. The only signs that anything is wrong is a strange form of tiredness and no recollection of having slept well the night before.

Stardate: 46192.3 Enterprise learns that a new crew member is really a member of the Q Continuum. However, she is unaware of her origins and her parents' rebellion against the continuum. When Q arrives to determine if she should continue to exist or not, things get strange for the Enterprise crew, and the nascent Q.

Stardate: 46235.7 After a transporter mishap changes Captain Picard, Ensign Ro, Keiko and Guinan back into physiological twelve year olds, while having no effect on their mental state. Things go even more wrong as a surprise Ferengi attack subdues the Enterprise's crew. Their apparent age, however, provides a substantial advantage in the effort to rescue the Enterprise from the Ferengi takeover.

Stardate: 46271.5 During some down time on the Enterprise, Geordi runs an experiment to see if Data has the memory capacity to act as a backup to the Enterprise's memory banks in an emergency. However, system problems then occur. Meanwhile, as Worf, his son, and Troi enjoy time on the holodeck, things go wrong there too. Data appears as the villain in their old west setting, and Worf learns the holodeck safeties are off, and there is no way they can exit.

Stardate: 46307.2 Capt. Picard and the crew must determine if certain mining machines qualify as "life forms", and whether they can be sacrificed to save humans on the mining site, when an emergency arises.

Stardate: 46357.4 Capt. Picard is reassigned, and a new captain joins Enterprise. Picard is assigned to lead a small Enterprise team on a dangerous mission, while the new captain causes great havoc among the remaining ship's crew.

Stardate: 46360.8 Capt. Picard is captured during his team's secret mission, and is tortured by the Cardassians, as Riker faces being relieved of command, and then later being asked to lead a separate mission to stop the Cardassians.

Stardate: 46424.1 The self-aware holocharacter, Sherlock Holmes' arch-nemesis Professor Moriarty, created in season 2's Elementary, Dear Data (02x03), reappears on the holodeck when Lt. Barclay performs a diagnostic check. Moriarty is able to take control of the Enterprise, and demands that the love of his life, Countess Regina Barthalomew, be given the same cognisance he has been given. However, is this really his true goal?

Stardate: 46461.3 Enterprise must investigate the disappearance of two crewmen on a subspace relay station. The mystery depends when evidence is found that the Klingons may have been involved. The mystery deepens even further when the Klingons produce one of the presumed dead crewmen, Lt. Aquiel Uhnari, who claims she fled the station after being attacked by the other crewman. The answer to the mysterious disappearance or passing of the remaining crewman puts Geordi's life, and the rest of the crews' life, at great risk.

Stardate: 46519.1 Troi awakens to discover she has been surgically transformed to look like a Romulan, as part of a plan to aid the defection of several high ranking Vulcan officials.

Stardate: (Unknown) Captain Picard is treated for a critical injury, which causes his artificial heart to fail and then appears to pass into the afterlife. There he finds Q waiting to greet him. Q provides Picard a chance to review and alter the events in his past which led to his having an artificial heart.

Stardate: 46578.4 Worf is told that his father was nothuged in a battle 25 years ago, as he had previously thought, but was captured and taken to a distant Romulan penal colony. Meanwhile, Data experiences disturbing visions.

Stardate: 46579.2 Worf discovers elderly Klingons are being held captive in a penal colony under the benevolent control of a Romulan governor.

Stardate: 46682.4 Captain Picard uncovers a plot to steal the highly dangerous compound trilithium from the starship's engines while it is in dry-dock for a procedure that requires all personnel be evacuated due to its life-threatening radiation. Unable to escape the ship, he must defeat the plotters before they are allhuged by the procedure. Meanwhile, the rest of the senior staff encounters problems of their own.

Stardate: 46693.1 - Picard must choose between love and command when he must make a decision that could place the woman he loves in a potentially deadly and high-risk mission.

Stardate: 46731.5 Enterprise races against the Cardassians and the Klingons to find the answer to a universal riddle. Capt. Picard is driven to find the answer to the riddle, as one of his favorite mentors' pursuit of this riddle has lead to his passing.

Stardate: 46778.1 Riker is put through the ringer when he is unable to discern if he is an insane patient on Tilonus IV, or is a member of the Enterprise crew performing a part in one of Dr. Crusher's plays.

Stardate: 46830.1 - Dr. Crusher puts her career on the line when she tries to clear the name of a cuddled scientist whose invention could allow starships to pass through a sun's corona.

Stardate: 46852.2 The ancient Klingon leader Kahless appears after Worf, in a Klingon trance ritual, tries to see his vision. However, the question becomes whether this is the true Kahless, or is he an imposter.

Stardate: 46915.2 - Riker discovers that eight years ago, an exact clone of him was created when he beamed through a planet's surface while returning to his starship. This clone, named Thomas Riker, has secretly remained on the planet for the past eight years, and still has romantic feelings for Troi.

Stardate: 46944.2 While Capt. Picard, Troi, Geordi, and Data are traveling in a long-range shuttlecraft they experience several time dilation events. As they return to Enterprise, they find it frozen in time in an attack by a Romulan ship.

Stardate: 46982.1 A strangely different Borg, who shows unknown before seen emotions, kidnaps Data. Enterprise chases after the ship Data is taken on, through a vortex, which leads them to a strange planet.