A cataclysm in the 24th century throws two ships back in time to the 23rd century, altering the course of history. With a different life where he never knew his father, James T. Kirk becomes a brilliant yet cynical misfit who is finally convinced to join Starfleet by Captain Christopher Pike in 2255. Three years later, Kirk, Vulcan First Officer Spock, and the young crew of the new USS Enterprise, with guidance from Spock's future self, must figure out a way to work together to prevent the one responsible for the death of Kirk's father, the future Romulan known as Nero, from destroying the Federation in a mad quest for vengeance.

A series of terrorist attacks on Earth places Captain James T. Kirk on a mission to deal with the culprit. Nothing is as it seems, as the Starship Enterprise is entangled in covert machinations to ignite war between the Federation and the Klingon Empire, with an ancient enemy in the mix. With alliances tested, relationships strained and differing motives clashing, how costly will the thirst for vengeance prove?

After stopping off at Starbase Yorktown, a remote outpost on the fringes of Federation space, the USS Enterprise, halfway into its five-year mission, is destroyed by a powerful, unstoppable wave of unknown aliens. With the crew stranded on an unknown planet and with no apparent means of rescue, they find themselves in conflict with a new ruthless enemy who has a well-earned hatred of the Federation and what it stands for.