Chakotay encounters Icheb and Naomi Wildman in Cargo Bay 2. Naomi is enjoying the puzzle they are playing with, as Icheb misunderstands it as a teaching tool. Chakotay tells Icheb of his cider stash and how he wishes Neelix will not find it. Icheb suggests storing it with the Borg spare parts as Neelix says they give him the creeps.
Later, a chronokinetic surge from a rift in space interacts with the warp core, and Chakotay is hit with a blast of temporal energy.
He awakens in the Doctor's sickbay and is astonished to discover the Doctor believes it is now several years earlier. Chakotay explores the ship and realizes that it is fractured into many differing time periods. The Doctor's treatment of him, realigning his body with a chronoton serum, allows Chakotay to pass through the time barriers.
During his exploration, he finds Engineering is under the control of Seska and the Kazon. He is beaten and detained, but manages to escape as the upper level of Engineering is in a different time period altogether. The bridge of the ship is a few days before the Caretaker incident, so Chakotay is regarded as a spy. He is again detained, and taken to the brig. He escapes when the security men who arrest him do not follow him through time, as they have not been injected with the Doctor's serum.
Chakotay gets the Doctor to produce a hypospray filled with the same serum he was injected with. He again finds Kathryn Janeway on the bridge. Janeway, a guard, and Chakotay talk in her ready room. Despite his knowledge of her past, he is not implicitly believed. He manages to take Kathryn hostage and injects her with the serum. They pass through a time barrier, leaving Janeway's guard Andrews unable to see her. This convinces Janeway to help Chakotay.
Their efforts reveal they must inject the serum into the bio-neural gel-packs on many areas of the ship. If successful, Chakotay will find himself in his right time and be able to stop the time-fracturing.
In the process, he refers to several episodes from the past seven years. Janeway begins to second-guess decisions she hasn't even made yet, especially after learning her human doctor will soon perish. She knows she started with 153 crewmen and struggles with wanting to know how many more she will lose. After a close encounter with the macroviruses, she becomes convinced that entering the Delta Quadrant at all is wrong, as it is a 'gigantic deathtrap'. Chakotay convinces her not to alter the timeline to avoid stranding the ship in the Delta Quadrant.
During the course of this they visit many areas and time periods. Cargo Bay 2 is from when the Borg have formed an alliance with Voyager. They meet Seven of Nine who is still part of the collective. Astrometrics, a section the younger Janeway did not know existed, is staffed by a much older Icheb and Naomi Wildman, both wearing Starfleet uniforms. Both are shocked as, according to their points of view, both Chakotay and Janeway had died long ago. Icheb reveals he had never exposed the location of the cider.
Both Astrometrics and Cargo Bay 2 have provided vital information to the problems, but the next few sections provide many dangers. The Transporter room is filled with angry Maquis, led by Torres, who do not trust the two. The holodeck, which is malfunctioning, is running a dangerous Captain Proton program, which Janeway must talk herself out of. Again, Chakotay must visit Engineering. He enters it alone. Seska decides to realign Voyager with her time period and use the knowledge of the future to guarantee she will keep control.
It does not work. Janeway had organized a resistance movement from all corners of time and ship. Borg-Seven, current Tom, early Harry, the Maquis and future Icheb and Naomi, all injected with Chakotay's serum, help defeat Seska's forces and allow the plan to go forward.
In a few seconds the ship is back to the original time and Chakotay manages to stop the disaster. When Janeway asks him why he turned the deflector dish into a giant lightning rod, he says he can't tell her because of the Temporal Prime Directive. Later, Chakotay has dinner with Janeway, who lets on that she knows the location of Chakotay's cider stash but can't tell him how she knows because of the temporal prime directive.