As the Equinox escapes, Voyager comes under attack by the nucleogenic creatures. Captain Janeway manages to get away with only superficial burns but Chakotay is knocked out. After Janeway remodulates the ship's shields to keep the extra-dimensional aggressors out, casualty reports come in reporting 13 wounded and two fatalities.
As Janeway walks down Deck 5 towards sickbay, she spots the body of a nucleogenic alien lying dead on the deck.
One of the injured crewmen dies in sickbay and we see Ensign Paris pulling a sheet over the disfigured crewman's head.
Equinox EMH - Portrayed by Robert Picardo. The Equinox's holographic doctor is of the same model as Voyager's EMH, but Captain Ransom deleted his ethical subroutines, removing his sense of morality and allowing him to conduct illicit experiments on the nucleogenic life-forms. In "Equinox - Part I", the Equinox doctor disabled Voyager's EMH and took his portable emitter, allowing him to beam over to Voyager as the Equinox's inside-man. In this episode, the Voyager EMH - who had been trapped on the Equinox - is able to return to his ship when Ransom decides to atone for his crimes by beaming over his crew to Voyager. The Doctor takes his sickbay back by deleting the Equinox EMH.
All the remaining Equinox crew who followed the mutinous Commander Burke are killed by the nucleogenic aliens when the ship's shields are disabled. Shortly afterward, the Equinox is destroyed when the aliens tear down the containment field for the warp drive.
The episode begins with a Vaadwaur city being bombarded from orbit. This occurs 900 years before the current series timeline.
Jisa - Wife of Gedrin, portrayed by Mimi Craven. She and Gedrin went into stasis at the start of the episode, but when Gedrin was woken by Seven, he found that Jisa had died after her stasis capsule had failed.
When Janeway learns of the Vaawaur's treachery, she attempts to leave them behind. A squadron of ancient Vaaduar fighters is launched and attacks Voyager as it takes off. Voyager destroys four of the attacking ships.
Voyager destroys three more Vaadwaur fighters as it reaches the planet's lower thermosphere.
Tuvok and Gedrin beam into the Vaadwaur underground bunker and Tuvok shoots a Vaadwaur soldier.
Gedrin uses an old Vaadwaur satellite to send targeting data to the Turei ships in orbit. The Turei then open fire on the Vaadwaur fighters pursuing Voyager, destroying six of them.
Voyager escapes from the Vaadwaur homeworld and goes to warp, leaving the Vaadwaur and the Turei to fight it out. The outdated Vaadwaur ships are severely outmatched by the Turei and several are destroyed as the two forces fight. It is unknown how the battle turns out.
No one dies in this episode, but Voyager makes another leap in its journey home. Using a form of interstellar catapult, Voyager crosses 30 sectors in just one hour and cuts three years off of its journey.
While no one dies in this episode, Paris, Chakotay, Kim and Neelix all suffer horrific hallucinations brought on by artificially implanted memories of a terrible massacre that occured on an alien planet. In the 21st century, 82 Nakan colonists were slaughtered when the Nakan military attempted to resettle them by force. Following the tragedy, a memorial monument was planted at the site of the massacre. This monument was a device that would implant the memory engrams of the soldiers who took part in the massacre into the minds of any beings who approached the planet, so that the events would always be remembered.
Chakotay, Paris, Kim and Neelix are aboard the Delta Flyer when the shuttle is captured by a Borg cube. The group later wake up inside an assimilation chamber and find a corpse lying on the surgical table, horribly mangled after a botched assimilation procedure.
When Voyager encounters the Borg ship that captured the Flyer, they detect only five drones aboard when there should be thousands. Seven later beams over to find the vessel riddled with corpses and the only living drones are children.
An examination of one of the Borg corpses reveals that the drone crew were wiped out by a spaceborne pathogen and that the juvenile drones survived because they were sealed within maturation chambers at the time of the infection.
After the death of the First, the remaining Borg children join the crew of Voyager.
Four of Twelve, Subjunction of Unimatrix Five-Two-Five - A Borg drone that appears in the episode's pre-title scene. This drone is one of many drones possessing a recessive mutation allowing them to enter the virtual reality of Unimatrix Zero during the Borg regeneration cycle. Four of Twelve is awoken from his regeneration period and brought before the Borg Queen who demands to know the interlink frequency that allows Unimatrix Zero to exist. However, Four of Twelve cannot tell her because "Zeroes" cannot retain their memories of Unimatrix Zero after awakening in the real world. The Borg Queen decides to try and extract the information from Four of Twelve's cortical array and orders her drones to dismantle him. Four of Twelve's severed head is later seen being dissected.
Voyager responds to a distress call coming from a colony on a lonely asteroid. By the time they arrive, they find the colony destroyed and no one left alive. Sensors detect residual Borg weapon signatures.
Seven enters her regeneration cycle and finds herself in Unimatrix Zero. She meets with one of its residents, Axum, who tells her about the virtual construct and how he and thousands of other mutant drones are able to visit it and exist as individuals. He goes on to tell Seven that the Borg have now detected Unimatrix Zero and are finding ways to identify mutant drones. Over two months, the collective has found and killed over 200 Zeroes.
While the Borg Queen examine's Four of Twelve's cortical array, two more mutations are discovered in spatial grid 649 (wherever in the galaxy that is). The Queen orders for the mutations to be deactivated and their cortical implants removed and examined. Later, the severed head of another drone is seen being examined in the Queen's chamber.
The Borg find a way to send drones into Unimatrix Zero to hunt down and identify the mutants. In the virtual world, the identification appears similar to assimilation in the real world as Borg attack the Zeroes and inject them with tubules. Once identified, the Zeroes vanish from Unimatrix Zero and awaken aboard whatever Borg ships they are on only to be deactivated.
Through the use of Tuvok's mind bridging technique, Janeway visits Unimatrix Zero along with Seven to meet Axum. During this meeting, the Borg enter Unimatrix Zero and Korok, a Klingon Zero, kills two drones with a bat'leth sword. It is unknown if the drones killed in Unimatrix Zero die in the real world too.
Korok is almost killed by a Borg and drops his bat'leth, but Janeway steps in and saves him, picking up the sword and killing the attacking drone.
Voyager attacks a Borg tactical cube on a mission to plant Axum's nanovirus into the Collective. Janeway, B'Elanna and Tuvok approach the cube in the Delta Flyer and match their transporters to the cube's shield frequency, allowing them to beam aboard. The Delta Flyer is detected by the Borg and destroyed just after the away team beam out.
After beaming aboard the Borg cube, the away team shoot two drones before the Borg adapt to their phaser rifles. Shortly after that, Janeway, B'Elanna and Tuvok are trapped within a shielded subsection and the Borg assimilate them. However, this is all a part of the plan...