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Season 1

Caretaker
A
Caretaker who is dying tries to find a genetic match by retrieving ships from every part of the galaxy. He pulls USS Voyager and Chakotay's Maquis ship from the Alpha quadrant. He is protecting the Ocampan people and worries that they will die if no one protects and care for them. After the Caretaker's death, Janeway has to decide whether to use the Caretaker's array to get her people home and destroy the Ocampa in the process or if she will destroy the array and make sure that the Kazon can't use it against the Ocampa.

 

The Cloud
Janeway wants to explore a
nebula emitting omicron particles, which might boost their energy reserves. She also hopes to find enough energy in the nebula to make coffey. When Voyager enters the cloud-like nebula it encounters an energy barrier that they have to break through using a photon torpedo. After investigating the nebula they realize that it is actually a living entity and that they have to repair the harm they've done to it.

 

Emanations
Chakotay, Kim and Torres find an alien burial ground on an asteroid and decide to observe only and return to Voyager to not desecrate the place. The problems start when Kim is pulled into a dimensional distortion and replaced by the body of a recently deceased woman. Kim finds himself on the Vhnori homeworld in another dimension.

 

Heros and Demons
When Voyager comes across a
protostar, Janeway has samples of its photonic energy beamed to engineering for study and for possible use in power converters. Harry Kim is nowhere to be found so Tuvok and Chakotay look for him at the holodeck where they discover that his holonovel (a version of the English epic poem "Beowulf") is running. They join in to fight the creature in the story and end up disappearing as well. It's then up to the EMH to locate the missing crewmembers at the holodeck and to rescue them.

 

Season 2

Non Sequitur
Harry wakes up in an alternate timeline where he works at Starfleet headquarters. Starfleet records shows that he never served on Voyager, which, as Kim well knows, has been reported missing in the Badlands. He also finds out that Paris isn't on the crew manifest; he's been paroled from the penal settlement that Janeway found him at and lives in Marseilles. Kim heads to France, looking for Tom, in hopes that they can help each other to restore the timeline.

 

Persistence of Vision
The crew finds themselves in the potentially dangerous Bothan space. Janeway is exhausted and is ordered by the doctor to take some "R&R" in the
holodeck. The Bothan representative gives the crew a chilly reception when he boards Voyager.
Before long, different crewmembers start to see people and visions from their past walking through the corridors. Kes is the only one who can see that these visions are hallucinations, and it is up to her to stop the effect the botha has on the crew.

 

Dreadnought
While serving in the
Maquis, Chakotay and Torres encountered the missile "Dreadnought", designed by the Cardassian and capable of mass destruction. Torres reprogrammed it to attack a Cardassian target instead of the Maquis.
When the missile was pulled by the Caretaker into the delta quadrant it headed straight for Rakosa, a heavily populated planet in the Delta Quadrant. Torres has to beam onto Dreadnought, where she gets the missile's computer system to stand down. However, after returning to Voyager, Dreadnought resumes its course for Rakosa.
Torres figures out that Dreadnought's computer thinks that Rakosa is an actual Cardassian target in the Alpha Quadrant, and that the Cardassians have found a way to feed it false information and forced Torres to cooperate with them. Torres must beam back to the missile and reprogram it before it's too late.

 

Deadlock
Voyager enters a plasma cloud to hide from Vidiian ships when Ensign Wildman goes into labor. Later the ship's warp engines stall, the antimatter supplies drain, proton bursts cause a hull breach, Kim is sucked out into space and Wildman's new born baby dies. Janeway realizes that a divergence field has duplicated all matter and that there isn't enough antimatter to sustain both vessels. She decides to go over to the duplicated Voyager and try to find a solution with the other Janeway.

 

The Thaw
Voyager detects bio patterns in stasis on an uninhabited planet. When they examine the stasis pods they find that the pods are programmed to open when the planet's environment has gone back to normal after a planet wide disaster. The crew tries to find out why the pods didn't open by sending Harry and B'Elanna into the pod's program. They realize that the program was designed to keep the inhabitants happy but their manifestation of fear has taken over the program and holds the inhabitants hostage.

 

Tuvix
Tuvok and Neelix becomes Tuvix after an accident with the transporters that mixed the two biological patterns together. Tuvix has distinctive personality traits from both crewmembers but is a totally new individual based on them both. Tuvix asks Janeway for the right to exist, which would mean that Neelix and Tuvok would be lost forever. She has to make the decision to separate Tuvix into Tuvok and neelix or to let Tuvix live.

 

Resolutions
An insect infects Janeway and Chakotay with an incurable virus during an away mission. The Doctor can't treat them and the two officers have to remain on a planet that blocks the progression of the fatal disease.
Janeway gives the crew orders to countinue to the Alpha Quadrant and puts Tuvok in command of the ship. The crew try to convince Tuvok to meet with a
Vidiian convoy, hoping that they might have a cure for the virus. Tuvok denies the request because Janeway has ordered them not to contact the Vidiians but Kim tries to persuade him to break the Captain's orders.

 

Season 3

The Swarm
Aliens materialize without warning on Paris' and Torres' shuttle, fire a weapon at them and disappear. Paris is seriously injured but Torres is able to navigate the shuttle back to Voyager. Neelix tells Janeway that he doesn't know these aliens by name, only by reputation. They attack ships that enter their territory, swarming in mass like insects. Charting a route around their huge territory isn't an option, so Janeway decides to stay on course.
The doctor doesn't remember how to perform the operation that will cure Paris. When Torres investigates, she realizes that the EMH's memory circuits are degrading. The only way to help him is to reinitialize his program, but that would mean loosing all memories the Doctor has acquired during the two years he has been active. When
the swarm attacks it is up to Kes to help the doctor.

 

The future's end part I and II
A federation timeship from the 29th century, piloted by Captain Braxton, is sent to destroy Voyager to prevent an accident occurring in the 29th century. Captain Braxton and Voyager are pulled into the
temporal rift and find them selves in 20th century earth. Janeway sends Tom Paris and Tuvok to earth to investigate who will cause the explosion in the 29th century and to find Captain Braxton. When they finally find him, as a homeless person, he explains that he crash-landed in the desert in 1967 where Henry Starling found the time ship and exploited its technology in order to start a high-tech empire. Starling, who has used up the technology he found on the ship is now planning to use Braxton's vessel to find more 29th century technology. They find that this action is the cause of the explosion in the future. They will have to stop him in order to restore the time line, prevent the explosion and to return to their own century.
The doctor receives his mobile emitter in this episode after being abducted by Henry Starling. Starling gives the doctor the mobile emitter he found in the timeship to allow the doctor to follow him around as his hostage. When Starling is defeated the doctor keeps the emitter and returns to Voyager.

 

Coda
Chakotay and Janeway crash land on a planet. After being killed by Vidiians they repeatedly find them selves on their shuttle after dying each time. After some time Janeway realizes that an alien presence is trying to lure her to her death and into his matrix by invading her cerebral cortex. She fights the alien and regains consciousness on the planet's surface, where she injured herself when crash-landing with Chakotay.

 

Blood fever
The Vulcan ensign Vorik asks Torres to be his mate, when she declines Vorik grabs hold of her face, but she succeeds to break free by dislocating his jaw. The Doctor explains that Vorik is going through a Vulcan mating ritual known as the Pon Farr. If he doesn't mate, he may die. Vorik attempts to get through the difficult period by engaging in intensive meditation.
Later, Torres, Paris and Neelix participate in an away mission to find gallicite. Torres is strangely aggressive, at one point viciously biting Paris on the cheek. Tuvok explains that Vorik initiated a telepathic mating bond between him and Torres. Now Torres is also experiencing the Pon Farr.
While searching for their missing crewmembers, Torres' Klingon instincts grow stronger and so do her suppressed feelings for Tom, but he refuses to take advantage of her. Vorik, who can no longer resist his instincts, joins them. He challenges Paris for Torres, but Torres takes up the challenge herself and engages in the ritual battle, overcoming Vorik. The blood fever purged, the Away Team returns to the ship.

 

Macrocosm
Returning from a trade mission to the
Tak Tak home world, Janeway and Neelix find Voyager adrift in space. They realize that many of the ship's systems are off-line. Neelix falls ill after being attacked by some kind of life form and Janeway goes to find an emergency kit. When she returns, he's gone. Janeway arms herself with weapons and goes to the Bridge, where one of the lifeforms known as macro viruses stings her. In the Mess Hall, she discovers unresponsive crewmembers and a giant flying creature, which tries to attack her. Janeway and the doctor must fight these life forms and free Voyager from infection before it's too late.

 

Real Life
The doctor creates his own picture perfect holographic family and invites Torres and Kes to dinner to meet them. Lieutenant Torres is unhappy with the unrealistic portrayal of family life and helps him create a more realistic family. Paris tries to collect a sample nearby an
Astral Eddy and gets pulled into the eye of the anomaly.

 

Season 4

Scorpion part I and II
Janeway makes a temporary alliance with the Borg to fight off
Species 8472 and is assigned a single borg representative - Seven of Nine-tertiary adjunct to unimatrix 01. When the drone jeopardises the safety of the Voyager crew they separate Seven of Nine from the Borg collective.

 

The gift
This is where Kes leaves USS Voyager and the series except for a brief return in 'Fury'. Kes informs Neelix and Janeway, that she must leave the ship due to the change she's undergoing. She uses a shuttle and then exists our reality, but takes Voyager with her, throwing them safely out of
Borg space - ten years closer to home. The doctor gives Seven a more human appearance by extracting the rest of her Borg implants, except for a small portion she can't function without. She starts to accept that she has been severed from the collective for good.

 

Day of honour
Torres and Paris have designed a holodeck simulation of the annual 'Day of Honour' ritual of self-examination and honor. As Torres is in a bad mood and not really up for the ritual, she fails and hides out in her quarters. When Paris comes to visit she pushes him away, afraid to accept the comfort of his friendship. In the meantime, Voyager encounters a
Caatati vessel, their commanding officer explains that they are one of few ships escaping Borg assimilation and that they have lost every thing. Janeway offers them what they can spare. In Engineering, Seven of Nine continues working on opening a transwarp conduit, but during the first test of the modifications, an accident occurs forcing Torres to eject the warp core.
Torres and Paris is instructed to retrieve the warp core by pulling it back to the ship with a shuttle craft but the Cataati steal the warp core and fires at their shuttle. They are forced to use environmental suits and beam out into space before the shuttle collapses. Certain that she will die without having the courage and honor to admit her love for Paris she tells him how she feels about him.

 

Random Thoughts
The crew was allowed to beam down to the surface of the Mari home world for rest and relaxation. A man bumped into B'Elanna, at a local marketplace, resulting in her thinking aggressive thoughts, but she didn't act on those thoughts. Those thoughts were believed to have triggered a murder that occurred later on and B'Elanna was arrested. Lieutenant Tuvok investigated the events, and discovered a black market of violent thoughts circulating the Mari Home world. B'Elanna was acquitted and freed from all suspicion.

 

Scientific methods
The
Srivani, alien scientists that uses the crew as guinea pigs for various medical experiments, invade Voyager. Janeway is forced to take extreme measures to free the ship. Tom and B'Elanna try to hide their budding relationship, which proves to be harder than they thought.

 

Vis a Vis
Voyager runs into a damaged alien vessel. The pilot is attempting to use an experimental propulsion system without success. Janeway transports him, Steth, and his prototype to Voyager. Paris, who has been restless and irritable lately and in need of a change, volunteers to help him repair his ship.
Steth breaks into Voyager's computer and downloads Paris' DNA information. Once Steth's ship is operational again, he overtakes Paris and switches bodies with him. Seth sends Paris away on his ship, and he stays on Voyager to live out Paris' life.

 

One
Voyager runs into a vast
nebula and everyone except for the Doctor and Seven of Nine are severely hurt by its radiation. Since it would take a year to go around it and only a month to pass through it, Janeway decides to put the crew in stasis and let Seven and the doctor take care of the ship. Every thing is doing well until the computer malfunctions and the Doctor and seven starts going on each other's nerves. Seven starts to have hallucinations and starts to doubt her abilities and the doctor's mobile emitter malfunctions leaving Seven alone to decide whether the hallucinations are real or not.

 

Season 5

Night
Voyager has entered a vast region of space with no star systems in sight for two years. The crew are slowly going crazy due to lack of stars and things to do. The only activity recorded is some high levels of theta radiation. Janeway stays in her quarters, thinking about the decision that stranded USS Voyager in the delta quadrant. When some injured night aliens intrude Voyager during a black out they realize that
Malon freighters are using the void as a dumping ground for their antimatter waste. The crew manages to leave the void, using the Malon spatial vortex, and seal it to stop more Malons form using it.

 

Once upon a time
Paris, Tuvok and Ensign Wildman's shuttle runs into an ion storm and crash lands on a
planetoid. As the crew prepares to go after the Delta Flyer, Neelix is in charge of keeping Ensign Wildman's daughter Naomi occupied. Buried three kilometres under the rock surface, Wildman is bleeding internally and needs surgery. Back on Voyager, they find no life signs when scanning the planetoid, but sends out rescue teams to find them. Naomi is worried when her mother doesn't call, but Neelix tries to distract her with a holodeck fairytale called "The Adventures of Flotter."

 

Extreme Risk
One of Voyager's probes gets stuck in a gas giant and is pursued by a
Malon freighter. Paris has conceived a new technologically advanced shuttle, the Delta Flyer, that can withstand the giant planet's atmosphere, and Janeway gives him permission to work with the rest of the crew on building it. Torres behaves strangely and withdraws from the others. She activates several holodeck programs but disengages the safety protocols. During such a program she is rendered unconscious and it is revealed that she has carried on in a similar fashion for several months. Chakotay tries to find out what is wrong.

 

Juggernaut
When the U.S.S. Voyager picks up a distress call, Janeway finds escape pods contaminated with Theta radiation. Two survivors, Fesek and Pelk, are beamed to sickbay as the crew discovers the source of the radiation is a disabled Malon freighter. The Malons explain that a theta radiation leak forced them to evacuate the ship. Fesek explains that when the ship explodes, the waste will ignite and destroy everything within three light-years and they have to board the Malon ship and disable it.

 

Season 6

Barge of the Dead
After a near-death experience in an ion storm, B'Elanna Torres meets her mother, Mistral, on the Barge of the Dead, which transports damned souls to Gre'thor, or
Klingon Hell. When she comes to in the sick bay B'Elanna tells Chakotay that she thinks she died and was on the Barge of the Dead. Later, after reading old Klingon scrolls, she tells Paris that she must have sent her mother to the Barge because of her own dishonour. B'Elanna believes that she can save her mother before she passes through the gates of Gre'thor but must first face her fears and her Klingon origin to restore the honour that was lost.

 

Dragon's Teeth
Voyager accidentally finds subspace corridors, belonging to the Turei, allowing them to travel 200 light years in 2 minutes. When Voyager must land for repairs the crew notice a decimated and burnt-out megalopolis. Scans indicate that the planet's civilization was destroyed by plasma-based weapons 500 years earlier. They find stasis pods and Seven of Nine activates one of the pod's reanimation sequence without Janeway's permission. The re-animated humanoid tells Janeway that the subspace corridors belonged to his people, the Vaadwaur, and not the Turei. After re-animating the entire hibernating waduaar population the Vaadwaur decide that they will take over Voyager to live more comfortably there (Dragon's Teeth).

 

Tsunkatse
Seven and Tuvok is kept prisoners by Penk, a
Norcadian, who forces people to fight each other against their will to make money. Seven is scheduled to fight in a game that will not stop until someone dies. The crew tries to free Tuvok and Seven before it is too late.

 

Season 7

Imperfection
Seven can't interface with her alcove and is forced to stay up all night in the mess hall. The Doctor realizes that Seven's
cortical node, which regulates her vital functions, is destabilizing and that she will die unless it can be replaced. Janeway orders Ensign Kim to scan a nearby Borg debris field and transfer the coordinates to the Delta Flyer, where she plans to salvage a replacement cortical node. Janeway and the Doctor practice the cortical node replacement operation several times in a holodeck simulation but fail each time. They realize that they can only use a cortical node from a living drone.

 

Shattered
Voyager's warp core begins to destabilize, and while Chakotay tries to maintain containment, an energy blast strikes him and knocks him out. When he wakes up in Sickbay he 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. When he enters the bridge he meets Janeway and the others at a time they still were in the Alpha quadrant and Chakotay still was a member of the Maquis. He realizes he's somehow been thrown seven years into Voyager's past and Voyager has been shattered into several different time zones. He administers the serum to Janeway and they have to work together to restore Voyager to it's original state.

 

Workforce part I and II
When Chakotay and Kim return from an away mission they realize that the crew is gone, the ship's heavily damaged and The Doctor is the only one remaining on the ship. They realize that the crew has been abducted and brought to
Quarra, a planet with a great labour shortage. Their minds have been purged of memories and they have been programmed to love their new home and work place. Chakotay, Harry and The Doctor have to find a way to bring their ship mates back from the heavily guarded planet.

 

Endgame part I
*** This synopsis is taken from startrek.com: ***
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 Korath, 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 Korath 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.

 

Endgame part II
*** This synopsis is taken from startrek.com: ***
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 Captan 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 d 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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