Spock, displaced in time, watches his closest friend heed his advice by allowing the love of his life to die in a traffic accident, thereby preserving Earth's history. Returning to the present, however, Spock confronts other such crises, and chooses instead to willfully alter the past. Challenged by the thorny demands of his logic, he will have to find a way to face his conflicting decisions.

The crew of the Nautilus, a battered Starship of mysterious origin, is beamed aboard the Enterprise. The group claims they are freedom fighters from the future working to save the Federation from the Consilium - a group of corrupt power-seekers. But when the Nautilus crew members suddenly seize control of the Enterprise, and a Starship from the future arrives to arrest the renegades, Kirk must separate his true allies from those who wish to destroy the Federation.

After defeating a hostile computer program guarding an abandoned Kalandan outpost, Captain Kirk and his crew attempt to unlock the secrets of an ancient artifact that had hurled the Enterprise more than one thousand light years in an instant.

In anticipation of a monumental conflict with the Klingon Empire, the Enterprise is assigned to guard a vital starbase located perilously close to Klingon space. But even as Kirk's mission brings him into a tense confrontation with an invading Klingon battle cruiser, an equally deadly menace lurks within the ranks of his own crew: Klingon infiltrator agents.

A science vessel is severely damaged during its mission to the Xondaii system and the Enterprise is dispatched to investigate and render assistance while Kirk, Spock and Sulu collect data on a nearby spatial rift.

Captain Kirk suspects that a new Klingon superweapon is the cause of the disintegration of a solar system, but the Prime Directive limits Kirk's ability to undo the disaster, and his humanitarian efforts spark hostility from Klingon warships.

On the Empyrea, a colony of genetically perfected human beings, McCoy discovers Anna, a daughter he never knew he had. McCoy soon realizes that the isolationist Empyreans must not learn her father is an off-worlder, and that her genes are less than "perfect." As relations with the Empyreans collapse around him, McCoy must find a way to save his newfound daughter from the harshest penalty her planet can impose.

After millennia of warfare, the planets Prastor and Distrel may have finally achieved a lasting peace. Investigating on behalf of the Federation, Captain Kirk is shocked to find out that the architect of the peace is none other than that notorious con artist, Harcourt Fenton Mudd! Mudd claims to be a changed man, but Kirk has his doubts.

As Spock, Sarek and Kirk struggle to preserve Vulcan's future, the planet's innermost secrets are laid before us, from its savage prehistory and merciless tribal warfare to the exploration of space and the development of o'thia -- the ruling ethic of logic.

An international consortium of the world's top scientists have conspired to create the Chrysalis Project, a top-secret experiment in human genetic engineering.

Forced to disguise themselves as interstellar traders, Captain Kirk and Mister Spock are trapped on the primitive world of Organia as Klingon Defense Forces occupy the planet. Determined to make the Organians see that they need not bow to oppression, the Starfleet officers sabotage Klingon materiel. In retaliation, the Klingon captain Kor executes many Organians.

For years, Starfleet Intelligence agents have carried out undercover assignments deep within the Klingon Empire. Surgically altered and rigorously trained in Klingon culture, they operate in plain sight and without any direct support, while collecting information and infiltrating the highest levels of imperial power. Their actions have given Starfleet valuable insight into the inner workings of Klingon government and its relentless military apparatus. After three of Starfleet’s longest serving agents fear exposure, they initiate emergency extraction procedures. Their planned rendezvous with the USS Endeavour goes awry, threatening to reveal their activities and the damaging intelligence they’ve collected during their mission.