While Icheb tutors Naomi Wildman in genetics and Chakotay joins Janeway for dinner, Voyager gets rocked by the gravimetric force of a spatial rift. Chakotay heads to Engineering when the ship's warp core begins to destabilize, and as he tries to maintain containment, an energy blast strikes him and knocks him out. Chakotay and the ship both shimmer in a strange patchwork effect. Torres checks Chakotay and sees that half his face is aged and the other half is youthful, and has him beamed to Sickbay. Chakotay wakes up in Sickbay and learns that his body was in a state of temporal flux, but the Doctor created a chronoton-infused serum that brought him back to normal. Chakotay asks the Doctor to come with him to check for other injured crewmen, but the hologram says he can't leave Sickbay. Chakotay asks about his mobile emitter, but the Doctor doesn't know what he's talking about. Chakotay can tell something is wrong and leaves.
Chakotay ascends in the turbolift and a distortion wave passes through it, causing the medkit he was holding to disappear. Chakotay enters the Bridge and asks Kim what's going on. Kim doesn't recognize him, but Janeway does, and orders guards to take him into custody, accusing him of sabotage on behalf of the Maquis. Chakotay realizes he's somehow been thrown seven years into Voyager's past. As he rides the turbolift with the guards, another distortion wave causes the guards to disappear. Chakotay then proceeds to Engineering and he finds it occupied by Kazon warriors and his old lover-turned-nemesis Seska. After they knock him out and revive him, Chakotay realizes he's in a time period five years ago when Seska (restored to Cardassian form) and the Kazon took control of Voyager. He tries to tell Seska what's going on, but she won't listen, so he has to bluff his way out of captivity. He manages to climb to an upper level in Engineering and passes through a distortion, and disappears from Seska's point of view.
Chakotay returns to Sickbay and tells the Doctor that the ship has somehow been fractured into different time periods, and that the serum injections seem to allow him to pass through the barriers between them. Chakotay asks the Doctor to give him the same serum in a hyospray that can also pass through the temporal barriers, so that he can put the ship "back together" again. He goes back to the bridge and approaches the Janeway of seven years past, telling her personal things about herself that he couldn't know. She starts to listen to his story and his plan, but still suspects him of nefarious intent, so he forces the serum injection upon her and takes her through a time barrier. Starting to gain her trust, Chakotay takes Janeway to the Astrometrics Lab which has temporal sensors that can help them map the time distortions. On the way they encounter injured crewmen in a corridor, in a time during one of Voyager's many predicaments, and Janeway gets increasingly perplexed. In Astrometrics, Chakotay and Janeway find a grown-up Icheb and Naomi 17 years into the future. They reveal that Chakotay and Janeway both died in the accident that shattered the space-time continuum aboard the ship. Janeway theorizes that if they can get to a section of the ship that still exists in the time period where the chronokinetic surge occurred, maybe they can counteract it. They could use the help of Seven of Nine — a name Janeway doesn't recognize — so Chakotay suggests finding her in another time frame.
Chakotay takes Janeway to the Cargo Bay where the Borg have entrenched themselves during Voyager's temporary alliance with them. Seven of Nine, who is still fully a drone, says a chronoton field generated by the warp core and projected throughout the vessel would force it back into temporal sync, and Chakotay would have a few seconds to counteract the energy surge that caused the problem. Janeway gets the idea of injecting the ship's bio-neural circuitry with the Doctor's serum in order to transmit the chronoton field. Chakotay and Janeway get the Doctor to replicate more serum, at which time the Doctor accidentally reveals to Janeway that the crew will get stranded in the Delta Quadrant.
Janeway and Chakotay begin going throughout the ship to inject the neural gel packs with the serum. In a corridor, they are chased by a macrovirus from another incident in Voyager's history in the Delta Quadrant, leaving Janeway further bewildered. They then enter a monochromatic environment in the ship's holodeck, which is Paris' "Captain Proton" program. Just when they find the panel they need, Doctor Chaotica and his henchmen appear and restrain them. Unable to deactivate the program, Chakotay tells Janeway to play along in the role of Arachnia, Queen of the Spider People. Rolling her eyes the whole time, she convinces Chaotica that she is loyal to him, and gets him to inject the gel pack himself.
In a transporter room, Janeway and Chakotay encounter several Maquis members, including Torres before she joined the Voyager crew. Torres accuses Chakotay of collaborating with the enemy, but he gains her trust and injects the gel pack. They next go to the Mess Hall, where Paris has set up triage for several crewmen injured in the original incident. Janeway finds her friend Tuvok, who is afflicted with radiation burns and dies while holding her hand. After leaving that location, Janeway tells Chakotay that she can't let all this happen again, and wants to put Voyager into temporal sync with her own time frame. She intends to change the future, the Temporal Prime Directive be damned. Chakotay sets her straight by pointing out that she's seen bits and pieces of the future, but not the whole picture. Despite the problems that Voyager has encountered, much has been gained through the crew's experiences, such as Seven of Nine recovering her humanity and Paris and Torres getting married, and the Maquis and Starfleet crews coming together under a captain who would never stop believing they would get home.
Their final stop is Engineering, where Chakotay has to deal with Seska. His story is so preposterous that she believes him, so she lets him inject the gel pack, but realizing that his presence means the Starfleet crew will regain control of Voyager, she demands that he modify the plan by bringing the ship into temporal sync with her time frame. He refuses, so she threatens to kill him. However, Janeway is waiting in the upper level, along with Paris and Kim who have been injected with the serum. They storm the Kazon contingent, and on that cue, the adult Icheb and Naomi rush in from one side of the room while Torres and another Maquis come in from the other side to surprise the Kazon and wrestle away their weapons. But Seska manages to grab Janeway and hold her hostage with a phaser. She demands inoculation for herself and her people, or Janeway will die, but at that moment Seven of Nine appears through a temporal barrier. Seska fires at the drone, but Seven's Borg forcefield repels the phaser shot and she overtakes the Cardassian, saving a thankful Janeway.
Janeway has everyone return to their section of the ship, pointing out that once the timeline is restored that will have no memory of what happened. Chakotay works the warp core as Janeway returns to the bridge. The chronoton pulse is initiated, and the ship is restored to the original time frame but a few seconds earlier. Chakotay immediately orders Torres to reroute main power to the ship's deflector so it can serve as a "lightning rod." The energy discharge from the spatial rift hits the deflector dish and burns it out, but the warp core is unaffected and the ship is saved. Chakotay refuses to tell the present-day Janeway why he made that order, invoking the Temporal Prime Directive, but that doesn't keep them from finishing their dinner together.