In the previous episode, Captain Janeway, B'Elanna and Tuvok were assimilated by the Borg. However, this was a part of their plan to introduce a nanovirus into the Collective that would allow the inhabitants of Unimatrix Zero to retain their individuality in the real world. The away team members were injected with a neural supressant prior to their mission that prevented their minds from succumbing to the Collective's influence, so while their bodies were assimilated, they retained their free will.
In Unimatrix Zero, Axum sets up several traps in the jungle to disable any invading Borg drones. One drone is seen pursuing a Zero and sets off a trap, causing a large log to swing down and slam into him.
The away team enter the central plexus of the Borg tactical cube and deploy the virus. Soon after, the Borg Queen takes notice as hundreds of voices within the Collective go silent. The Queen identifies one drone within her own chamber in the Unicomplex who has disconnected from the hive mind, and when she questions him he attacks her. The drone is unable to harm the Queen as a forcefield appears between them and the Queen has two still loyal drones drag the Zero away.
Aboard Tactical Cube 138, Captain Janeway is apprehended after Tuvok succumbs to the Collective. She is forced to communicate via hologram with the Borg Queen who resides at the Borg Unicomplex and she shows the captain the result of her actions. The drone that had previously attacked the Queen now lies dead on the floor after being deactivated.
Cube 630 - A Borg vessel in an undetermined area of the galaxy. Manned by 64,000 drones, the Borg Queen has lost contact with three of them. In order to stop these rebel drones from freeing any others, the Queen commands the cube to self-destruct, killing its entire crew compliment.
Sphere 878 - A Borg ship manned by 11,000 drones. Only one drone aboard this ship is a Zero, but the Queen nevertheless commands this vessel to self-destruct and kills all of them.
Axum and Seven meet again in Unimatrix Zero and Axum informs her that the Borg Queen has been destroying whole ships to eliminate a handful of Zeroes. Over the course of three hours, 11 ships have self-destructed.
B'Elanna clubs a Borg drone in the head with a piece of debris.
The Zeroes abandon Unimatrix Zero and the virtual construct is erased, but the Borg resistance movement continues. A bitter Borg Queen attempts to deny Voyager its captain back by triggering Cube 138's self-destruct system. However, Voyager manages to beam the away team back just before the cube explodes.
At the beginning of Part 1, two Hirogen hunters are gunned down by their prey: four Starfleet officers hiding in a pond. While they appear to be human, these figures are actually holograms.
Voyager approaches a Hirogen space station and the away team sent over finds the interior to be a holographic simulation of a forest. Tuvok discovers two dead Hirogen lying in some underbrush, possibly the same two killed in the pre-title scene.
After the simulation is shut down, the away team stand within a vast hologrid surrounded by dozens of dead Hirogen.
Voyager and a Hirogen vessel pursue a ship commandeered by holograms. When they catch up to it, it turns out to be a decoy and explodes when the Hirogen approach it. It is unknown how many Hirogen are killed.
After the Doctor is abducted by Iden, he is implanted with the memories of another hologram that had suffered multiple violent deaths at the hands of the Hirogen. In a 'dream', he witnesses other holograms being hunted and killed before being slashed and gutted by a Hirogen Alpha.
Iden transmits a feedback surge along Voyager's deflector pulse which threatens to overload the warp core. B'Elanna erects a forcefield around the core and stabilises systems, but not before a yellowshirt is killed by an electrical surge from his work station.
Iden's ship attacks a Nuu'bari vessel in order to "liberate" its holographic labourers and destroys the alien ship after the holograms are transferred to his ship's databanks. Much to B'Elanna and the Doctor's disgust, the deaths of the two Nuu'bari aboard that ship were for nothing as the liberated holograms were only simplistic automatons and were incapable of becoming sentient.
After the Hirogen vessels are disabled, Iden's followers transport them to the surface of a Y-class planet with a toxic atmosphere. They then beam a holographic generator to the surface so they can go down there to hunt the Hirogen as they were once hunted.
Two Hirogen try to take shelter in a small cavern, but their holographic pursuers - a Starfleet redshirt and a Borg drone - simply walk through the rock and shoot the Hirogen from behind.
A Hirogen Alpha throws a rock at a hologram but the rock just passes through him. The redshirt hologram responds by shooting the Alpha.
When Voyager is pulled into the anomaly known as "The Void", they are swiftly attacked by another vessel trapped like they are. The vessel steals much of Voyager's fuel and food supplies and as their situation deteriorates, Janeway gives the order to track down the alien scavengers and take back the stolen resources. Unfortunately, when Voyager catches up with the ship, it is on fire and there are no lifesigns. Evidently they were attacked by another vessel trapped within the Void.
Janeway manages to establish an alliance with several aliens trapped in the Void, but one of these allies violates the alliance charter by stealing technology from a non-allied ship and then killing the people he took it from. This occurence is not shown.
This is the final episode of Star Trek: Voyager, marking the Voyager crew's triumphant return to the Alpha Quadrant.
In Admiral Janeway's future, it took Voyager a total of 23 years to get home. During this period, the ship lost 47 of its crew, including Seven of Nine. Chakotay also died some time after Voyager's return, consumed by grief over Seven's loss.
When Admiral Janeway arrives in the past, she urges Voyager to seal the temporal rift she came through. Two Klingon vessels are pursuing the admiral but it is unknown what becomes of them as the rift is closed while they are inside it.
Using technology provided by Admiral Janeway, Voyager flies through a Borg-occupied nebula containing a transwarp hub, a vast array that supports the Borg's galaxy-wide transwarp network. Using futuristic transphasic torpedoes, Voyager obliterates two attacking Borg cubes.
Admiral Janeway flies into the transwarp hub and travels to Unimatrix 1 where she confronts the Borg Queen. The Queen attempts to assimilate her, but in doing so contracts a neuralytic pathogen that the amiral injected herself with before departing Voyager. The pathogen causes the Borg hive-mind to become fragmented, leading to the destruction of countless Borg ships and the Unicomplex itself, crippling the Borg Collective and possibly even wiping it out.
Voyager flies into the transwarp hub while the Queen is occupied with the admiral and destroys the interspatial manifolds that support the hub, causing it to collapse.
One Borg sphere is able to comply with the Borg Queen's last command before she dies and pursues Voyager through transwarp, almost capturing it. After they exit the transwarp conduit,Voyager launches another transphasic torpedo into the sphere's interior and destroys it.
Voyager emerges from transwarp right where they had hoped to be: the Alpha Quadrant. Surrounded by Federation ships and with Earth in clear sight, the USS Voyager's long journey at last comes to an end.