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| # | Air Date | Title | |
| 146 | 09/04/96 | Basics, Part II | The Doctor and Suder, secretly still on Voyager, plot to overcome the Kazon. Their acts of sabotage are almost discovered, and the Doctor is disabled, leaving Suder to disable secondary phasers before he is discovered and killed. As Tom arrives with the Talaxians, the rest of the crew struggle to survive the planet's dangers and primitive natives. |
| 145 | 09/11/96 | Flashback | A repressed memory threatens to cause permanent brain damage for Tuvok, and a mind meld he has with Janeway to discover the cause takes them both to his past where he was serving with Captain Sulu. |
| 147 | 09/18/96 | The Chute | Tom and Harry are imprisoned after being falsely accused of bombing a city they are visiting. Tom is badly attacked and Harry struggles to keep him alive and find a way out. |
| 149 | 09/25/96 | The Swarm | The Doctor's program is beginning to deteriorate, and to repair him, a holographic program of his creator is consulted. In the meantime, Voyager is under attack by an alien species that swarm onto the ship and drain energy. |
| 144 | 10/02/96 | False Profits | When Voyager detects Alpha Quadrant technology, they stumble upon a planet who worships two Ferengi as gods. Unable to persuade them to leave, Neelix is sent to impersonate the Grand Nagus, and when that backfires, the crew attempts to draw upon prophecies to convince them to leave. |
| 148 | 10/09/96 | Remember | In B'Elanna's dreams, she lives the life of visiting Enaran woman and discovers the secret that the Enarans committed an act of genocide. |
| 143 | 10/30/96 | Sacred Ground | When Kes falls into a coma after wandering into a Nakami shrine's force field, Janeway endeavors to go through their ritual to find the secret of how to cure Kes. |
| 150 | 11/06/96 | Future's End, Part I | Voyager finds its way to Earth, but in 1996, and the effort of getting back causes them to become tangled up with a capitalistic CEO of a tech company who's gotten his hands on 29th century technology. |
| 151 | 11/13/96 | Future's End, Part II | As Voyager fights to prevent the launch of the 29th century time ship, the Doctor is kidnapped and given a holoemitter and Chakotay and B'Elanna crash land somewhere in Arizona. |
| 152 | 11/20/96 | Warlord | The consciousness of a tyrannical alien takes over Kes' body and has big plans for his reign of terror. |
| 153 | 11/27/96 | The Q and the Grey | Q offers Janeway to be the mother of his child, who he thinks will be the key to bringing peace to the Q Continuum, torn by a civil war. |
| 154 | 12/11/96 | Macrocosm | The Doctor inadvertently brings to Voyager a virus that has evolved to grow into large airborne objects that infect and terrorize the crew. |
| 156 | 01/08/97 | Fair Trade | When Neelix becomes desperate to find a map of a nearby region of space, he is reacquainted with an old friend, Wix, who went to prison for a crime they both committed. Owing a debt to him, Neelix keeps quiet about a murder Wix commits during a drug trade. Their trouble eventually leads Tom and Chakotay to be falsely arrested. |
| 155 | 01/15/97 | Alter Ego | Harry falls in love with a holographic character who later becomes infatuated with Tuvok. To keep their friendship and to keep Harry from feeling betrayed, he deletes the character, but she later appears in Tuvok's quarters and seems to be preventing Voyager from leaving a nebula. |
| 158 | 01/29/97 | Coda | Janeway and Chakotay's shuttle crash land on a planet, and Janeway has an out-of-body experience where she sees her own death, eulogy, space burial, and a visit from her dead father. |
| 157 | 02/05/97 | Blood Fever | [synopsis] B'Elanna's mating instincts are switched on thanks to Vorik's pon farr just as she ends up becoming trapped in an underground cave with Tom. |
| 159 | 02/12/97 | Unity | When Chakotay responds to a Starfleet distress signal, he finds a colony of ex-Starfleet officers that were assimilated by the Borg, and are now disconnected and trying to forge a new home for themselves. |
| 161 | 02/19/97 | Darkling | The Doctor's attempts to tweak his behavioral subroutines goes awry and he develops a sinister alter ego bent on taking over the Doctor's mild-mannered self. |
| 160 | 02/26/97 | Rise | Neelix, Tuvok and a Sklar, Nezu alien, crash land on the Nezu planet and must reactivate an unused elevator tower that leads to a space station for help. Sklar then appears to be poisoned after hearing something on the roof, and when Tuvok goes to investigate, Sklar tries to push Tuvok off and sabotage the mission. |
| 162 | 03/19/97 | Favorite Son | Taresians, a species mostly of amorous women, convince Harry that he is one of them and that he should stay, at least to learn about his people. But when Voyager returns for him, the aliens prevent them from doing so. Meanwhile, Harry realizes men are only needed for genetic material and will be later killed. |
| 163 | 04/09/97 | Before and After | Kes finds herself living her life backwards, jumping from the time of her death to brief sequential periods of time preceding that, and she has to find a way to get her crewmates to help. |
| 164 | 04/23/97 | Real Life | The Doctor decides he wants to create a holographic family for himself, and after B'Elanna makes a few realistic modifications to the program, he realizes having a family isn't as easy as he thought it would be. |
| 165 | 04/30/97 | Distant Origin | A race of humanoid dinosaurs discover the remains of one of Voyager's crew, and become convinced that humans are their distant ancestors. |
| 167 | 05/07/97 | Worst Case Scenario | What starts off as a harmless -- and even intriguing -- tactical training holodeck program turns deadly when the crew realizes that Seska managed to hijack it back when she was on board and turned it into a way to get her revenge. |
| 166 | 05/14/97 | Displaced | One by one, the crew is transported off the ship and replaced by a group of aliens intent on taking over Voyager. |
| 168 | 05/21/97 | Scorpion, Part I | Dangerously close to Borg space, Voyager encounters Species 8472, who they realize is a much greater threat and have no choice but to forge an alliance with the Borg to defeat them. |