This series follows the adventures of the Federation starship Voyager, isolated tens of thousands of light-years from home. In this episode, a spatial phenomenon causes the ship to be fractured such that different parts exist at different points in time and Commander Chakotay must fight old adversaries in order to get Voyager restored to normal.
While Commander Chakotay is discussing with Icheb and young Naomi Wildman where to hide a special stash of cider from Neelix, the U.S.S. Voyager is stuck by a chronokinetic surge from a rift in space interacting with the ship's warp core. Chakotay is struck with a blast of temporal energy. He gains consciousness in Sick Bay where the Doctor has injected him with a chronoton serum to repair injuries from the temporal blast. As Chakotay talks with the Doctor, he finds the Doctor believes it is several years earlier. Chakotay goes exploring the ship, and discovers that various sections of the ship are experiencing different periods of time, a result of the chronokinetic surge. The chronoton serum enables Chakotay to see and travel between these periods, but not other members of the crew.
During his exploration he finds that Engineering has been taken over by Seska and other Kazon, and though captured, he managed to escape due to his ability to travel between these time periods. He makes his way to the bridge, which is currently set a few days before Voyager was taken to the Delta Quadrant and before he joined the crew. Captain Janeway immediately identifies him as a spy despite his plees, and ordered to the brig, but en route, they pass through another time period, which Chakotay passes into but not his captors. Chakotay returns to Sick Bay and has the Doctor create more of the chronoton serum, then returns to bridge, injects Janeway with the serum, and takes her to another time period to avoid capture.
Janeway is initially hostile towards Chakotay's actions, but he demonstrates what has happened to the ship and she becomes more trusting of him. They happen upon Astrometrics, which is set many years in the future as it is manned by Icheb and Naomi Wildman, both adults, who are surprised by their appearance, as in their timeline Janeway and Chakotay had died several years earlier. The two are able to provide Chakotay with details on the chronokinetic surge and suggestions for how to restore Voyager to normal, and Icheb alludes that he never revealed the location of Chakotay's cider stash. Later, they enter Seven of Nine shortly after her arrival on Voyager, and her Borg knowledge provides a plan for restoring the ship to normal; if Chakotay injected the chronoton serum into the ship's organic gel-packs with the chronoton serum, all parts of the ships will align with Chakotay's timeframe.
As Chakotay and Janeway travel through the time-separated ship to enact this plan, Seska discovers their intent, and decides to use the same plan to align the ship to her period, thus allowing her to control Voyager using knowledge from the future to assure she maintains control. Seska has had herself and several of the Kazon injected with the chronoton serum, allowing them to take control of other parts of the ship, but because of Chakotay and Janeway's tour of the various time periods of the ship, they have been able to convince most of the other crew to work against the Kazon. Chakotay successfully injects the serum across the ship, and the ship is fully realigned to his time period with all individuals returning to their respective times. He finds he has ended up moments before the chronokinetic pulse is due to strike. He quickly orders Lt. Torres to blow out the ship's deflector, which prevents the interaction that caused the time fractures.
Later, Chakotay and Janeway have dinner together, where Chakotay tells Janeway he cannot reveal why he ordered the deflector blown out due to the Temporal Prime Directive. He is surprised that Janeway knows of his cider stash, but Janeway refuses to answer, claiming she too is under the Temporal Prime Directive.