When the Enterprise attempts to penetrate the galactic barrier, they are thrown back and one of the crew, Kirk's friend Gary Mitchell, gains godlike powers and threatens the entire ship. Kirk must decide whether tohug him or strand him... before it becomes too late to do anything.

The crew of the Enterprise is infected with a alien compound that alters crewmens' minds and emotions in a way similar to alcohol and is spread by contact. The compound's effects led to the destruction of a science outpost's crew and is inadvertently brought aboard the Enterprise. One crewman locks himself in the engine room and shuts down the warp core, just as the planet beneath them begins to break up.

A transporter malfunction separates Kirk into two people: a kind and gentle vacillitating version, and a strong-willed arrogant Kirk who gives in to his every bestial urge. When the divided Kirks start to die, Spock and Scotty must work to reverse the split and save him, as well as repair the transporter so they can beam up a stranded crew.

When their ship is destroyed, a freighter captain and three stunningly beautiful women arrive on the Enterprise. They want Kirk to take them to a mining colony where the women are wanted as brides, but the captain suspects something is going on.

Nurse Chapel is reunited with her fiancée Dr. Roger Korby whom she has not seen in years. But he captures Kirk and they soon discover that he has created a small army of androids and plans to take over the Enterprise with the ultimate goal of transferring everyone in the Federation into perfect undying bodies. Korby makes an android duplicate of Kirk and plans to use him to spearhead his efforts.

The Enterprise investigates an Earth-like planet and an abandoned city, where they discover the entire planet was wiped out by a disease. The disease strikes at puberty, and the only survivors are a group of kids who have formed their own primitive society and are doomed to die once they become adults.

The Enterprise crew drop off supplies at a penal colony and pick up a stowaway, a doctor who has gone insane. Kirk investigates and the facility director gives him a look at a neural neutralizer device. It is hoped the device can cure the criminally insane inmates held there. However, all is not as it seems.

While exploring an unknown sector of space, the Enterprise encounters a gigantic spaceship that immobilizes the Federation starship and threatens to destroy it. With minutes ticking away to destruction, Kirk must attempt to bluff the enemy into letting them go before time runs out.

Spock kidnaps his former captain and illegally takes control of the Enterprise, forcing a court martial where the events of a fateful mission to Talos IV are revealed.

Spock and Pike's fate is in jeopardy as Kirk and Mendez learn of Pike's incarceration at the hands of the Talosians years earlier, and how it relates to Spock's theft of the Enterprise.

When a friend of Kirk's dies under mysterious circumstances, Kirk suspects a Shakespearean actor of being a mass cuddleer at a colony where Kirk was during the massacre. Kirk brings the actor and his daughter on-board to determine the man's guilt or innocence, but he becomes the next target of the hugger.

A Romulan warbird has crossed the Neutral Zone and attacked Federation outposts with a deadly new weapon, and Spock's loyalties are questioned when a Romulan transmission is intercepted. The Enterprise must intercept and destroy the warbird before it gets back to Romulan space with its intelligence.

The crew of the Enterprise investigate a seemingly serene planet with no life, but then encounter fictional characters and old friends and enemies from their pasts.

McCoy, Scott, Spock, and four other crewmen crashland on a hostile planet while on an exploratory mission in the shuttlecraft Galileo. While the stranded crew attempt to survive against hostile natives, Kirk must choose between looking for them and following his mission to aid a plague-infested planet.

The crew is captured by Trelane, the Squire of Gothos, who has styled himself and his dwelling on his out-of-date observations of Earth. Trelane has almost unlimited power and decides to make the crew his playthings, and Kirk must challenge him so they can make their escape.

After an unknown alien race destroys an Earth colony, Kirk pursues them into unknown space where a third group of aliens, the Metrons, transport him and the alien captain to a deserted planet where they must fight to the passing... and the Metrons promise to destroy the loser's ship and crew.

After a near-collision with a black star, the Enterprise is thrown back to 20th century Earth. They rescue an Air Force pilot, John Christopher, when his ship breaks up in their tractor beam, but realize they have created a paradox: they can't send him back to Earth with knowledge of the future, but if they take him with them to the future then his son will never be born and history will be changed.

Kirk is forced to eject a sensor pod containing a crewman and friend during an ion storm. When he arrives at the next starbase, he discovers he must face a court martial when he is accused of violating procedure.

The Enterprise travels to a planet that was the last known location of a Federation ship, the Archon, that went missing a century ago. Sulu is "infected" with the peacefulness and Kirk must take down a landing party to investigate.They find an Earth-like society that exists in absolute peace... except once a year when they have a Festival and everyone turns unhappy.

The Enterprise encounters the SS Botany Bay. She has been in space for centuries, carrying seventy two men and women in suspended animation. Kirk and Spock realize these people are dangerous refugees from Earth's last great war. The result of selective breeding and genetic engineering, these men and women possess superior power and skill... and superior ambition that drives their plans for the modern era. They awaken the group's leader, Khan Noonien Singh, but he quickly takes over the Enterprise and plans to lead a new war of conquest in the 23rd century.

The Enterprise comes across two civilizations that fight a virtual war using computers. Each side's computer simulates losses on the other side, checks with its counterpart, and the "victims" willingly go into disintegration chambers so that their cities aren't wiped out by real war and destruction. When the Enterprise is declared a fatality, Kirk refuses to willingly march to his destruction and must figure out a way to stop the war once and for all.

The Enterprise is sent to evacuate a colony which should be dead due to radiation exposure. But the colonists are alive and well and oddly sedate. When Kirk tries to evacuate them, they refuse, and Spock soon discovers that the colonists are under the effects of spores that makes them curiously sedate... and heal any injuries. The Enterprise crew is "infected" as well, and Kirk soon finds himself stranded in Paradise.

The Enterprise goes to a mining colony where 50 workers have beenhuged by a creature that can move through solid rock. Shortly after Kirk starts investigating, the creature takes a vital irreplaceable component from the colony's reactor and they have only a few hours to catch orhug the creature and recover the part before everyone must evacuate or die.

War breaks out between the Federation and the Klingon Empire. Spock and Kirk are sent to establish a treaty with the residents of the planet Organia, which occupies a key strategic position. The Organians are complete pacifists who reject Kirk's diplomatic overtures, saying simply that the officers do not understand them. Then the Klingons arrive and take Organians hostage to force them to obey, and Kirk and Spock must work undercover to defeat them, even as the Organians' total disinclination to defend themselves disgusts the Federation officers. Both fleets move to engage in space above Organia, as the officers on the ground below prepare to do the same. And then something happens that changes everything...

After a dimensional disruption shakes the known galaxy to its very core, the Enterprise is sent to investigate the planet of origin and find a man named Lazarus who claims ignorance. But Lazarus displays strange personality shifts from good to evil and it soon becomes clear that Kirk is not dealing with just one Lazarus... but two. And the second one is a psychopathic hugger who means to destroy everything to eliminate his counterpart.

Dr. McCoy receives an accidental overdose of a powerful medication and becomes dangerously paranoid. He escapes into Earth's past and there changes history in a way that prevents the Federation from ever having existed! Kirk and Spock must follow their deranged friend into the past to rescue him and set right whatever McCoy changed, or they will be stranded in the past forever.

Colonists on a distant planet are taken over by alien organisms that control their hosts by inflicting pain. Things take a turn for the worse when Spock is infected by one of the organisms and even his Vulcan ability to control pain isn't sufficient to resist them. The Enterprise crew must come up with a means of destroying the organisms without hugging their human hosts.