The USS Enterprise is on patrol near the Romulan neutral zone and the crew is experiencing unusual dreams. Captain James T. Kirk and Science Officer Spock both confess that they are having dreams that Spock is Captain of the ship and Kirk is an Ensign. Kirk informs Spock that Starfleet intelligence has discovered that the Romulans are attempting to use time travel and are sending more ships to investigate. Captain Kirk goes to sleep, and awakes as Ensign Kirk on the VSS ShiKahr, which appears to otherwise be the Enterprise. The Ensign is a drug addled ex-convict who has been on board for only a day.

The Romulans had attempted to travel back in time and destroy the Federation, but they instead created a Federation dominated by Vulcans. They shielded a ship from the changes and compare the differences, realising that it needs to be reversed. Meanwhile, Captain Spock begins to act protectively of Ensign Kirk, but the Captain is injured on an away mission. After Doctor McCoy conducts a series of mental scans, the crew of the ShiKahr realise that history has been altered. The Romulans plot to use Kirk to force Spock to impersonate their leader. Spock mindmelds with Kirk, each realising their personas from the main timeline.

Romulan agents board the ShiKahr and capture Kirk. Spock agrees to their demands and travels with them. Whilst en route, Spock enters pon farr and finds that he is linked to Kirk, but mates with the Romulan Thea to allow it to pass. They retrieve Kirk, and discover that taking Kirk and Spock was a ploy to have them both travel back in time to stop the Romulan agents from preventing the formation of the Federation. They travel back in time and disable the agents, but Spock is seriously injured and dying. Kirk and Spock mindmeld as reality shifts once more and restores the original timeline.