Kirk, now an Admiral, retakes command of the refitted Enterprise to stop a hostile and sentient massive energy cloud advancing toward Earth.

While exploring test sites for the Genesis terraforming project, the U.S.S. Reliant is hijacked by Khan Noonien Singh, bent on revenge against Kirk who frustrated his plans to seize control of the Enterprise fifteen years earlier. Khan attacks the Enterprise on a training cruise with inexperienced Starfleet cadets led by Kirk who has not commanded a starship for some time.

Concerned about McCoy's unstable condition since Spock's death, Kirk learns that in his final moments, Spock transferred his katra, or spirit, to the doctor. To reunite Spock with his soul, Kirk must violate a quarantine law and steal the Enterprise to retrieve Spock's body from the rapidly dying Genesis planet.

Kirk and his crew head for Earth to stand at their court martial for the theft of the Enterprise, and its subsequent destruction, when they find Earth under siege by a giant probe transmitting a destructive signal—intended for the extinct humpback whales. Kirk takes his crew back to the late 20th century to retrieve some whales so they can respond.

Exiled from Vulcan, Spock's emotional half-brother Sybok believes he is called by God and hijacks the partially-retrofitted Enterprise-A to take it to the Great Barrier at the centre of the Milky Way to meet his maker, while an ambitious young Klingon captain sets his sights on Kirk.

After their homeworld is wracked by an environmental disaster, the Klingons attempt to make peace with the Federation though many on both sides are opposed. Just before the summit conference, Kirk and McCoy are arrested for the murder of the Klingon chancellor.

An energy ribbon cuts a swath through the galaxy on the day of the maiden voyage of the newly commissioned Enterprise-B, and Kirk is presumed killed in an encounter with it. 78 years later, Picard and his crew race against time to stop Tolian Soren, a scientist intent on deflecting it into a planet to gain immortality inside it.

The crew of the Enterprise-E pursues the Borg back in time as they threaten to prevent first contact between Humans and Vulcans, thus destroying the Federation before its founding.

The crew of the Enterprise aids a rebellion on the Baku homeworld against Picard’s superior officer, Admiral Dougherty, who wants to relocate the Baku to gain possession of the medicinal cosmic radiation that floods their planet.

Captain Picard confronts the villainous new Reman leader Shinzon, a younger genetic clone of himself who kidnaps Picard to replenish his own DNA and uses an earlier prototype of Data to spy on the Enterprise while plotting to destroy Earth.

Fresh from Starfleet Academy, James T. Kirk, Spock, and the rest of the Enterprise crew must stop Nero, a Romulan from the future whose quest for vengeance threatens the Federation. The movie creates an "alternate reality" for the Enterprise and its crew that frees the film and the franchise from continuity issues.