Admiral Janeway beams aboard Voyager and meets her younger self, and is moved to see a healthy Tuvok and Chakotay again. In Janeway's Ready Room, the Admiral reveals to the Captain that Voyager did eventually make it back to Earth after another 16 years, and the ship became a museum on the grounds of the Presidio. But the Admiral came to tell Captain Janeway to take Voyager back to the nebula as a shortcut home, using technology she brought to get past the Borg. The Captain wonders why she would want to tamper with the time-line, but the Admiral asks for her trust. In Sickbay, the Doctor confirms that the Admiral is genetically identical to the Captain, but 26 years older. He has also detected an implant in her brain, which the Admiral reveals the Doctor himself invented in the future to allow her to pilot a vessel with a neural interface. Seven of Nine enters — to an emotional greeting from the Admiral — reporting that the armor and weapons technology on the shuttle can be adapted for Voyager, and the Captain orders it done.
The crew busily upgrades the ship with the futuristic technology, and feels optimistic they might actually make it home this time. When Seven takes a break to regenerate, she is visited in her mind by the Borg Queen, who warns her not to let Voyager return to the nebula or it will be destroyed. Seven wakes up violently in her sparking alcove, and upon being cared for by the Doctor, reports the Queen's warning to the two Janeways. The Admiral insists the Borg are 30 years behind compared to the technology and tactics she's brought, so the Captain maintains course for the nebula.
When Voyager approaches the murky nebula, Captain Janeway orders the armor deployed, and the ship's hull is completely covered. Three Borg Cubes engage the starship, but their weapons fire is repelled. They scan the ship, then focus their fire on a specific section of the armor which weakens it. Voyager responds with the launch of transphasic torpedoes, which completely obliterate the Cubes with one or two shots each. Voyager then finds the center of the nebula, where the crew sees a massive Borg structure. Admiral Janeway orders Paris to enter an aperture in the structure, but Captain Janeway belays that order until she gets an explanation. Seven of Nine reveals the structure is a transwarp hub, one of only six in the galaxy. Angered that the Admiral didn't tell her about this, she orders the ship out of the nebula.
The crew learns the hub connects thousands of transwarp conduits to endpoints in every quadrant of the galaxy, perhaps the most significant tactical advantage the Borg have. Captain Janeway wants to know how to destroy it. But Admiral Janeway strongly objects to any such attempt, and insists on taking the ship home before the Collective can counteract the armor and weapons. The Captain pulls the Admiral aside and wonders how she got so cynical, arguing that they have a chance to save millions of lives. The Admiral reminds her of the decision that got her ship stranded in the first place, putting the lives of strangers ahead of her own crew. The Captain is willing to make the same kind of decision, but then the Admiral tells her that Seven of Nine is going to die. And her husband, Chakotay, will never be the same, and neither will Janeway. Along with 22 other casualties, Tuvok will succumb to a degenerative neurological condition that he hasn't told her about. She can prevent all that and get home today safe and sound.
Captain Janeway approaches Tuvok about his condition, and learns he can only be cured by mind-melding with members of his own family. But she also learns that Tuvok would rather destroy the hub than save himself. Even Seven of Nine refuses to listen to the Admiral's argument. In fact, the entire crew agrees that they'll allow their journey to take longer if they can accomplish something they believe in. The Admiral had forgotten how much the crew loved being together, and admits she was wrong to talk the Captain out of something she had set her mind to. But then the Captain proposes that there might be a way to "have their cake and eat it too."
The Admiral boards the shuttle, and the Captain injects her with a hypospray. The Admiral takes the shuttle through one of the hub's apertures and enters the Unicomplex where the Borg Queen resides. Using her neural interface, she enters the mind of the Borg Queen and tries to make a deal with her, in order to save the Voyager crew from themselves. She wants the Queen to send a Cube to tractor Voyager back to the Alpha Quadrant, in exchange for telling her how to adapt to the transphasic torpedoes. But the Queen detects the Admiral's shuttle, beams her over and injects her with assimilation tubules. Meanwhile Voyager deploys its armor and enters one of the transwarp hub's apertures. While the Admiral is being assimilated, the Queen orders vessels to intercept Voyager. But she realizes she no longer has control over the Collective. She realizes that when Admiral Janeway was assimilated, she released a neurolytic pathogen into the Collective, designed to bring "chaos to order." While in a transwarp corridor, Voyager launches its transphasic weapons and begins to collapse the transwarp hub. The Borg Queen, meanwhile, begins to literally lose parts of her own body as her Unicomplex begins to crumble in an array of explosions.
In the Alpha Quadrant, Admiral Paris and the present-day Barclay detect a transwarp aperture opening up less than a light-year from Earth, and every ship in range is ordered to converge there. In the collapsing transwarp corridor, a Borg Sphere bears down on Voyager as its armor begins to fail. Captain Janeway orders Lt. Paris to adjust course. The Borg Sphere emerges into the Alpha Quadrant and Starfleet vessels begin firing upon it. But then it explodes in a spectacular fireball, and Voyager emerges from within the debris intact. Admiral Paris welcomes Janeway back home, and she promises him a full report. Meanwhile, a baby is being born in Sickbay — Tom and B'Elanna's daughter. Paris is dismissed from his duties so that he can meet his new child and Captain Janeway orders Chakotay to take the helm and set a course for home. The Starfleet armada then escorts the long-lost Voyager back to Earth.