It is the 10th anniversary of the U.S.S. Voyager's triumphant return to Earth after 23 years in the Delta Quadrant. Kathryn Janeway is an admiral, Harry Kim is a starship captain, Tom Paris is a full-time holonovelist, and the Doctor is married to a human woman and has named himself "Joe." At a reunion party, Admiral Janeway talks with B'Elanna Torres, who is now Federation Liaison to the Klingon High Council, about arranging a political favor for a Klingon named Korath. Later, the admiral serves as guest lecturer in Commander Reginald Barclay's Starfleet Academy class about the Borg, but when a cadet asks a question about Seven of Nine, Janeway evades the subject. She's pulled away from class to receive a message from Ensign Miral Paris, the daughter of Torres and Paris, who is on a secret mission to arrange some sort of exchange between the admiral and Korath.
Admiral Janeway stops to say goodbye to Tuvok at his hospital room where he is suffering a neurological disorder that has destroyed his mind, telling him she may never come back. She then has the Doctor over to her apartment and asks him to procure for her a supply of Chronexaline, an experimental drug that can protect biomatter from tachyon radiation, for "classified" reasons. She arranges to get some downloaded information and a shuttle from Commander Barclay, and finally she visits Chakotay's gravesite, promising that when she's through things will be better for everyone.
Twenty-six years earlier, when Voyager is still in the Delta Quadrant, the pregnant Torres is having repeated occurrences of false labor, and Seven of Nine is developing a serious romance with Chakotay. Tuvok is concerned when he is defeated by Icheb in Kal-toh, so he visits the Doctor and learns his neurological condition is slowly deteriorating. Seven is playing Kadis-Kot with Neelix by remote when she is interrupted by the detection of high neutrino emissions indicative of a wormhole. Seven later tells the crew that the center of a nearby nebula may contain hundreds of wormholes, any of which could lead to the Alpha Quadrant.
Back in the future, the Doctor visits Tuvok, who has become increasingly agitated about the "disappearance" of Admiral Janeway, and blurts out that she's never coming back. Curious, the Doctor visits Commander Barclay to get in touch with Janeway, and Barclay says simply that she's out of town. But when Barclay starts stammering, which he hasn't done in years, the Doctor knows he's hiding something. Meanwhile Admiral Janeway has taken the shuttle to a moon where she meets up with Miral Paris, who introduces her to the House of Koroth. After dismissing the Ensign, Janeway meets with Koroth, who has something for her but demands information on her shuttle's shield modifications. The admiral won't go beyond the original terms of their agreement, so she is shown out.
In the present time, Voyager enters the murky nebula and barely misses colliding with a Borg Cube. Captain Janeway orders the ship out of the nebula, refusing to go back despite Ensign Kim's appeal to not give up on those wormholes. Later, Seven asks the Doctor to perform a procedure he devised to remove a failsafe device in her cortical node, so she can pursue more intimate relationships — specifically, with Chakotay.
Admiral Janeway tells Koroth she's "reconsidered" his offer — she'll give him the shield emitter, but first she has to inspect the device he's offering. Korath allows her to scan the device, whereupon Janeway attaches a transport enhancer to the device and beams it and herself to the shuttle. The enraged Klingons send one of their futuristic ships to fire upon her, but Janeway deploys a new armor technology around the shuttle that absorbs the phaser blasts. She jumps to warp and escapes, but when she arrives at her destination, she is met with the Federation starship Rhode Island, commanded by Captain Kim, who orders her to stand down. Kim has learned of her plan from the Doctor, who coaxed it out of Barclay, but Janeway insists the consequences are too great if she doesn't follow through, and asks him to trust her judgment one last time. Kim helps her prepare Korath's device — a chrono-deflector which is now affixed on top of the shuttle — and realizes it will burn itself out with one use. Janeway already assumed this would be a one-way trip. Unable to talk her out of the scheme, Kim beams back to his ship, and Janeway activates the chrono-deflector. Two Klingon ships decloak and begin firing, and Janeway is unable to deploy the ablative armor. The Rhode Island comes back and distracts the Klingons while Janeway activates a tachyon pulse.
Meanwhile on the present-day Voyager, Seven of Nine and Chakotay are having their first kiss when they are summoned to the Bridge. Some sort of temporal rift is forming in front of the ship, and Klingon weapons fire is being detected. But then a Federation vessel comes through the rift and hails Voyager. Captain Janeway sees the older version of herself on the viewscreen, ordering her to emit an anti-tachyon pulse from the deflector to close the rift before the Klingons come through. Startled, the Captain hesitantly fulfills that order and seals the rift, then asks what the hell is going on. Admiral Janeway says she's come to bring Voyager home. What she doesn't realize is that the Borg Queen is monitoring her transmission.