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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.
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