Barely an hour after being marooned on a primitive planet by the Kazon, Voyager's crew start suffering casualties. Ensign Hogan (portrayed by Simon Billig) is killed by a giant serpentine creature while gathering bones at the entrance to a cave. Only is uniform is left.
Tom Paris, who had boarded a shuttle shortly before Voyager was captured, is on his way to meet with a Talaxian colony to request help. On the way, he is attacked by a Kazon raider. He is able to fight back when he reverses his shuttle's engines and lets the raider overtake him; he then fires on the raider's engines and destroys it.
Kes and Neelix are captured by the primitive natives of Hanon IV. When Chakotay organizes a rescue, he has Tuvok and several other crewmen standing by with bows and arrows should the natives become hostile. The primitives chase after Chakotay, Neelix and Kes and so Tuvok fires on the closest native, planting an arrow in his chest.
Chakotay's group are forced to flee from the Hanons by entering the cave where Hogan was killed. They discover a giant eel-like creature resting inside and try to find a way around it. Unfortunately, a blueshirt loses his footing which causes the creature to stir from its slumber. The unfortunate blueshirt is swallowed whole.
Lon Suder and the Doctor are the only crew members left on Voyager after the Kazon commandeer the ship. Since the Doctor cannot leave sickbay, Suder is forced to run interference and sabotage by himself. Much to his anguish, he has to kill a Kazon guard to secure weapons and he drags the body through the Jefferies tubes to sickbay to keep the other Kazon from finding it.
After the Doctor is disabled, Suder is left with the trying task of retaking Voyager himself. Fortunately, while he is disrupting the ship from within, Lt. Paris leads a squadron of Talaxian ships to attack it from without. Suder sneaks into Main Engineering with a Kazon disruptor and shoots every Kazon in the room, allowing him to reach a control console to shut down Voyager's weapons array.
Suder's sabotage of the phaser array results in a catastrophic overload when the Kazon try to fire on Tom's shuttle. The overload causes several small explosions on the bridge, killing several Kazon.
Kes, while being possessed by the mental essense of Tieran, shoots an Ilari ambassador the second he materialises in the transporter room. She also shoots the transporter operator.
Tieran bursts into the Imperial Hall on Ilari and shoots the Autarch and all of his guards.
One of Tieran's aides voices his concern that Tieran cannot maintain control of Kes, urging the tyrant to find a new host body. Tieran becomes enraged and punishes the servant with a fatal psychic attack, causing him to bleed out of every orifice in his head.
Captain Janeway, Chakotay, Neelix and Demmas storm Tieran's throne room, shooting all of his guards.
Voyager is infested by a macrovirus, a viral organism that has evolved to incorporate the growth hormones of its hosts. The macroviral organisms can grow up to a meter in size and Captain Janeway encounters one such creature in the messhall, blasting it with a phaser rifle.
In a flashback of the initial outbreak, the Doctor studies a macrovirus in sickbay and it rapidly grows to the size of a basketball. Luckily the Doctor synthesizes an antigen grapples the macrovirus in his hands so he can inject it with the antigen. The antigen kills the macrovirus immediately.
Janeway tries to reach Deck 12 through the Jefferies tubes in order to to use the environmental systems to deliver the macroviral antigen across the whole ship. She encounters three of the large macroviruses in a junction and blasts them with her phaser rifle.
Just before Janeway can administer the antigen, Voyager is attacked by the Tak Tak, an alien race she and Neelix had gone to negotiate with before the outbreak. The Tak Tak captain tells Janeway that they purified the mining colony where the macrovirus was discovered, meaning that they destroyed the colony and killed everyone there to stop the virus from spreading.
Since the macrovirals are drawn by infra-red signatures, Janeway remotely activates the holodeck in order to lure the virals into one spot. The macroviruses start attacking the holographic characters, unable to tell the difference between hologram and living organism.
Janeway nears the holodeck with a makeshift bomb that will disperse the antigen. She is attacked by a stray macrovirus and she kills it by grabbing one of its tentacles and then stabbing the creature with a knife.
Janeway throws the antigen bomb into the holodeck and eradicates the macroviruses.
Neelix finds himself involved in an illicit trade deal with an old friend of his, a Talaxian called Wixiban. The two Talaxians meet with a shady alien aboard a space station who then attempts to kill them after recieving his merchandise which, as Neelix only realises after the deal turns sour, is narcotics. Wixiban takes Neelix's phaser and kills the dealer.
Neelix gets a canister from Bahrat filled with tainted warp plasma and deactivates the safeties. The narcotic suppliers, led by Tosin, arrive to meet with Neelix and Wix. When Tosin accepts the canister he realizes that it is worthless but Neelix quickly tells him the canister has been leaking plasma into the room and any energy discharge from his weapon will ignite the entire section. Bahrat arrives and attempts to arrest them but one of the suppliers fires anyways and the ensuing plasma fire knocks Neelix unconscious and vaporises the shooter.
No characters die in this episode, however Voyager arrives at a planet that had once been home to a race called the Sakari. The colony was destroyed 60 years prior to the episode's events, and at the very end of the episode, Chakotay shows Captain Janeway a horrific find: the skeletal remains of a Borg drone. This marks the first appearance of the Borg in the Voyager series.
Voyager encounters a heavily damaged Borg cube adrift in space. They find that the ship and its drone compliment all ceased functioning five years previously after being caught in an electrokinetic storm which severed its link with the Borg Collective, which explains why the Borg have never salvaged the vessel. B'Elanna reports that there were 1,100 bodies on board.
A Borg corpse is brought aboard Voyager and the Doctor and B'Elanna conduct an autopsy. During the procedure, the Doctor accidentally triggers a backup power cell that revives the drone. The drone is quickly deactivated before it can pose a threat to anyone.
Manipulated by the Cooperative, Chakotay reactivates the neural-field generator aboard the Borg cube, allowing all of the former Borg on the planet to become connected with each other. However, this also causes the cube to power up and all the dead drones to reactivate.
Before the Borg cube can threaten Voyager, the Cooperative use their new neural link to trigger the vessel's self-destruct sequence. Voyager just manages to get clear before the cube explodes.
In this episode, Kes is experiencing moments of her life backwards beginning from her near-death at old age of 9 (which is elderly by Ocampan standards). In one of these temporal shifts, she discusses a time when she was exposed to some form of radiation. Tom remembers it as the "Year of Hell", a time when Voyager was under constant attack by aliens called the Krenim. During that period, Captain Janeway and B'Elanna Torres were killed.
After several time-jumps, Kes arrives at the beginning of the Year of Hell and witnesses the deaths of Janeway and B'Elanna. Both women are standing over a console that explodes when the ship is struck by a chroniton torpedo, killing them instantly.
Voyager destroys the attacking Krenim ship by firing their phasers at the Krenim's torpedo launchers just as they fire.
Including Janeway and Torres, Voyager lost 11 crew members during its battle with the Krenim.
Kes is brought back into temporal sync while she is at the age of 3 (the present at this point in Voyager's journey). The events she experienced in the future have not yet happened, though the Year of Hell will take place in Season 4. However, Kes will not be a part of it as she will leave the ship before then.
At the beginning of the episode, two Borg cubes are destroyed by an energy discharge fired by an off-screen adversary.
As Voyager enters Borg space, it encounters an armada of 15 Borg cube-ships. The Borg fleet ignores Voyager and moves on, but Voyager maintain a sensor lock on them. Some time later, the Borg armada's power signatures cease. When Voyager investigates, they find that all of the Borg cubes have been destroyed. Some portions of the cubes are intact and are still manned by living drones.
Chakotay, Kim and Tuvok beam aboard one of the wrecked Borg vessels to investigate an abnormal alien biomass. When they beam aboard, they find that most of the drones are either dead or damaged and malfunctioning.
Chakotay, Kim and Tuvok discover a pile of dismembered Borg corpses aboard the damaged cube. The heap of body parts is reminiscent of a psychic vision experienced by Kes.
Inside the organic spacecraft, Tuvok finds a dead Borg drone that appears to be infected with some form of alien tissue.
A ten-foot tall alien creature smashes through a bulkhead and kills two Borg drones. It also strikes Harry and infects him with invasive cells that start to slowly eat him alive. This creature is later identified as "Species 8472", as the Borg call them.
When Voyager enters a Borg-held star system, Janeway tries to negotiate with the Collective by offering them tactical knowledge that can help them defeat Species 8472 in exchange for safe passage through their home territory. During the negotiation, ten alien bio-ships emerge from a quantum singularity and combine their energy to destroy an entire planet. The Borg planet explodes and the shockwave engulfs two cube ships attempting to flee.