Voyager and the Borg cube are pursued by a Species 8472 bioship. The alien vessel fires a bio-plasmic blast and blows a sizeable chunk out of the cube. On the inside, a Borg drone is flung from its alcove.
As the bioship closes in, the Borg cube maneuvers itself between the attacker and Voyager, sacrificing itself to protect the Starfleet vessel. The cube collides with the bioship and both vessels are destroyed, but Captain Janeway, Tuvok, Seven of Nine and a contingent of drones beam over to Voyager at the last moment.
The war between the Borg and Species 8472 continues to go badly for the Collective as another skirmish between the two enemies appears to be one-sided; a Borg ship is seen destroyed and others heavily damaged while Species 8472 suffers no casualties at all.
Seven of Nine is informed by the Collective of Species 8472's progress. They invade yet another Borg-held system, destroying eight planets, 312 ships and exterminating 4,000,621 drones.
When the Borg seize control of Voyager's deflector dish to create a singularity leading to Species 8472's home-space, Chakotay has the cargo bay depressurized, venting the drones out into space. Only Seven of Nine survives.
Four bioships attack Voyager after it enters fluidic space. By then, Voyager have developed a biomolecular weapon based on modified Borg nanites that is capable of affecting the aliens. The biomolecular warheads do not have an immediate effect, but a few seconds after impact the bioships are suddenly corrupted by the Borg nanoprobes and explode.
When Voyager returns to the Delta Quadrant, a fleet of bioships descends upon them. A high-yield nanoprobe warhead is fired that destroys 13 bioships in a single blast. This deters Species 8472 from continuing their war and they return to their own dimension.
No one dies in this episode, but a number of important events occur. Kes' psychic powers are enhanced exponentially and she begins to transform into a higher state of being. Her transformation threatens to destroy Voyager, and so she leaves the ship. However, she offers her friends one final gift before they part: her new powers allow her to throw Voyager far beyond Borg space and take them ten years closer to Earth. Meanwhile, Seven of Nine has been severed from the Borg Collective and becomes a permanent member of the crew.
Voyager makes first contact with a race known as the Caatati. Rahmin, captain of the Caatati ship, tells Captain Janeway that his planet was conquered by the Borg a year ago and only a few thousand escaped with minimal resources.
The alien hologram Dejaren is seen dragging a dead Serosian through the halls of his ship at the start of the episode.
The Doctor and B'Elanna make contact with Dejaren who tells them that all six members of his ship's crew had been infected and killed off by a virus, leaving him alone on the ship. It is later discovered that Dejaren lied and actually murdered his crew.
An alien race called the Srivani covertly conduct experiments on Voyager's crew. In the latter half of the episode, one such experiment kills a crew member by causing all of her blood vessels to rupture at once.
The "Year of Hell" event previously seen in the episode "Before and After" occurs, albeit differently than Kes had experienced.
Day 1 - The episode begins with a Zahl colony being completely erased from existence by Annorax's temporal weapon ship.
Day 4 - After a minor encounter with an inferior Krenim ship, Voyager is later engulfed by a temporal shockwave caused by Annorax's temporal weapon after it fired on the Zahl homeworld. The Zahl race is completely erased from time and the Krenim vessel harassing Voyager becomes much more threatening. Voyager is badly damaged by the Krenim's chroniton torpedoes and a blueshirt turns up dead on the bridge.
Day 32 - Voyager destroys an attacking Krenim ship by deploying four photon torpedoes like mines.
Voyager suffers structural collapse on Deck 5, resulting in the deaths of two crew members.
Day 47 - No deaths occur this day, however Tuvok is blinded when an undetonated Krenim torpedo lodged in a Jefferies tube explodes in his face.
Day 65 - Annorax uses his temporal weapon to erase a race called the Garenor from the timestream. The consequences of removing the Garenor include deleting much of the Krenim Imperium as well, eradicating all of its colonies and most of its ships. By this point,Voyager is protected by temporal shielding and is not affected by the chronometric shockwave generated by Annorax's weapon ship. Shortly afterwards, Voyager is intercepted by Annorax and Chakotay and Paris are abducted.
Day 73 - Voyager is left in tatters with half the ship rendered uninhabitable with life-support failing on the remaining decks. The surviving crew are forced to abandon ship and split into groups while Captain Janeway and the senior staff remain on Voyager and attempt to stop Annorax.
Day 133 - Voyager's situation deteriorates further when the ship takes cover inside a nebula. The ship's ventilation systems are unable to keep out the nebula gases, leading to several decks being flooded.
Day 180 - Voyager is struck by a stream of micro-meteoroids while the engines are down. Captain Janeway tries to correct the engine problem from Deflector Control, but the section is on fire and extinguisher systems are non-functional. Using a large piece of shrapnel as a shield, Janeway braves the fire and re-initializes the main deflector, but suffers terrible burns which the Doctor cannot fully heal.
Day 207 - Annorax erases the Ram Izad race from history with his temporal weapon.
Day 228 - Captain Janeway forges an alliance with two races: the Mawasi and the Nihydron. They prepare to bring the fight to Annorax and stop him from further corrupting history.
Day 257 - The final day of the Year of Hell. Voyager and its new allies attack Annorax's ship. Two Nihydron vessels are eradicated by the temporal beam before Paris, who is still aboard the weapon ship, disables its temporal core. The vessel switches to conventional weapons and fires on a Mawasi vessel, causing it to collide with Voyager and tear off a sizeable chunk of the primary hull.
Janeway decides to collide Voyager with the weapon ship, believing that destroying it will completely reverse all of the alterations Annorax has caused to the timeline. This gambit pays off; as soon as the weapon ship explodes, history returns to normal. Annorax and his wife still live happily on Kyana Prime, the Krenim Imperium is still a significant power and Voyager navigates around Krenim space, thus ensuring that the Year of Hell never occurs.
In this episode, Voyager encounters a telepathic race called the Mari who have eliminated crime and violence on their world by outlawing all violent thought. When B'Elanna is accidentally nudged by a passing Mari in a marketplace, she momentarily thinks of lashing out. This thought is apparently responsible for the man who bumped into her later beating a man in the middle of the street and an elderly woman stabbing and killing a grocery vendor the next day.
Using a network of alien subspace comm relays, Voyager transmit the Doctor to a Starfleet ship in the Alpha Quadrant to send a message. When the Doctor arrives aboard the USS Prometheus, he finds that the crew are all dead and the ship has been commandeered by the Federation's long-time adversaries, the Romulans.
This episode marks Voyager's first contact with the Hirogen, who control the sensor network the Starfleet crew are using.
Back in the Alpha Quadrant, the Doctor and the EMH Mark-2 have released a gaseous anaesthetic throughout the Prometheus, incapacitating the Romulans. Three Romulan warbirds arrive shortly after followed by three Starfleet ships, and a battle begins to decide which side will claim the Prometheus.
The two medical holograms fumble with the Prometheus' bridge controls and inadvertantly activate the prototype ship's multi-vector assault mode, splitting the ship into three individual modules. The doctors command the computer to target the Romulans and the Prometheus destroys one of the warbirds. The other Romulan ships retreat, allowing Starfleet to retake the ship.
The Doctor succeeds with his mission and contacts Starfleet Headquarters, informing them of what has happened to Voyager since its disappearance. Now that Starfleet are aware of Voyager's situation, they are able to commit resources to assist with the ship's return to Earth.
On their way to one of the Hirogen relay stations, Voyager finds an alien ship adrift in space. The ship's only occupant is dead, apparently having had his entire skeleton and all internal organs removed.
Voyager recieves a datastream from Starfleet via the Hirogen relay station, containing numerous leters from the families and friends of the crew. Chakotay recieves a letter from a former colleague stating that the Maquis resistance has been destroyed following the Cardassians' alliance with the Dominion. Only a handful of Maquis have survived and are in Federation custody.
Voyager disrupts the stability field of the Hirogen relay station, causing the micro black hole powering it to consume it from within. The Hirogen ships attacking Voyager are also consumed by the black hole and the entire relay network is disabled, cutting off Voyager's only link to the Alpha Quadrant.
Voyager encounters a Hirogen ship drifting through space with its defences down. Chakotay, Tom and Tuvok beam over to find out what happened and Tom finds a Hirogen helmet lying on the floor. When he picks it up, he is shocked to find it still attached to a severed head. A tricorder scan reveals that the Hirogen hunter was physically ripped apart.
The surviving Hirogen hunter is rescued by Voyager and tells them that it was tracking powerful prey. That prey soon boards Voyager and the crew are shocked to find that it is a Species 8472 pilot. A Hirogen hunting party attacks Voyager and demands the return of their hunter and the alien creature. After establishing telepathic contact with the creature, Tuvok states that it was abandoned when the rest of its kind retreated to fluidic space after their failed war with the Borg. The creature only wants to return to its realm, but Seven of Nine is convinced that continuing to protect it will only result in Voyager's destruction, and so she defies Captain Janeway and transports the 8472 pilot to one of the Hirogen ships. The Hirogen then leave Voyager be and take their hunter and the creature, most likely killing it.
Many of the deaths that occur in this episode are merely holographic characters generated on the holodeck.
In a Klingon simulation, Janeway is made up as a Klingon and clubs an opponent with a spiked mace.
While the Doctor is treating Seven in sickbay, he complains to the Hirogen alpha Karr about the number of patients he's had to care for in a twelve-hour cycle: almost 30 casualties, one of which does not survive.
After they took over Voyager, the Hirogen took advantage of Federation holo-technology to satisfy their pursuit of the hunt. They subject the crew to various simulations, most notably a recreation of World War II, and use neural interface devices to make the crew believe they are characters in the simulations and also turn off the holodeck safeties, making all of the simulated battles as dangerous as the real thing. They even enlarge the hologrids by installing new holo-emitters throughout the ship. However, after a huge explosion in the WWII program damages the main hologrid, the holographic characters are able to leave the confines of the holodeck thanks to the new emitters throughout the ship.
Janeway shoots two Nazi soldiers that walk out of the holodeck.
Ensign Kim is almost shot by a Nazi soldier, but Lt. Paris appears behind him and shoots the Nazi with a 9mm pistol.
Five Hirogen hunters are killed as the battle in the holographic Sainte Claire rages on.
Chakotay and the bridge crew are cornered by the Nazis who prepare to execute them. However, Neelix and the Doctor bring in a group of Klingons from another simulation who start attacking and slaying the Nazis.
Voyager attempts to travel through a Mutara-class nebula, but the nebula contains traces of lethal radiation which begin immediately affecting the crew as the ship enters the cloud. One unfortunate yellowshirt suffers horrific radiation burns and dies.