(written from a Production point of view)
Voyager's sixth season was the first to be televised without running concurrently with seasons of Star Trek: Deep Space Nine, and can be characterized as having the feel of being oddly disconnected from seasons four and five that preceded it. As a result, season six could be said to have more in common with the story-telling of season one, being populated by numerous episodes with story lines wholly independent of each other and the greater series arc, which by this point, was very well established. There are of course exceptions, most notably in "Pathfinder" when real-time communication is made with Starfleet, with the help of an obsessed Reginald Barclay. However, it was not until the end of the season in "Life Line" that this significant plot development was revisited.
Numerous new aliens were introduced throughout the season, again indicative of the reliance on wholly independent story lines. However, the Hirogen make a re-appearance in "Tsunkatse", the Klingons in "Barge of the Dead", the Borg make a (by now familiar) resurgence in "Survival Instinct" and the season finale "Unimatrix Zero". Happily, the Vidiians also return in "Fury", as does a vengeful Kes intent on sabotaging the ship, killing B'Elanna Torres in the process. Only one of the newly-introduced alien species (the Hierachy) reappeared later, in the seventh season episodes "The Void" and "Renaissance Man".
Worthy of particular note is the introduction of the treacherous (and hugely popular) Vaadwaur in "Dragon's Teeth". While being vaunted as a possible season six nemesis during a conversation towards the end of the episode, it was perhaps a missed opportunity on the part of the show's producers that the possibility of having the Vaadwaur return later on, was never taken up;
"I doubt we've seen the last of them."
- - Janeway, to Seven of Nine ("Dragon's Teeth")
"Collective" halfway through the season added a significant development to the evolution of the series as Voyager's crew manifest grew by four with the introduction of the "Children of the Borg". Story lines featuring the children served as an addition to Seven of Nine's learning curve, as she took on the role of surrogate mother to the lost, and disconnected children. Although never directly spoken of in the script for either episode, with the knowledge of hindsight it is possible to note that in "Child's Play", a surreptitious link to the series finale "Endgame" is planted when Icheb's parents send him back to the Borg full of neurolytic pathogen. It is this same pathogen that Admiral Janeway uses when assimilated by the Borg Queen during the climax to the series finale, which infects the Collective and disables the transwarp hub, enabling Voyager to return home, and deal a crippling blow to the Borg at the same time.
A couple of small "jumps" closer to home were realized in the episodes "Dragon's Teeth" and "The Voyager Conspiracy" but nothing like the huge leaps which helped characterize the previous two seasons, and for the majority of season six, any significant "jumps" forward were missing, again likening the sixth season to the first.
The process of overcoming the difficulty in portraying Janeway as both authoritative and feminine that had dogged most of the first four seasons may have begun with season five's "Counterpoint" and her dalliance with the Devore Imperium's Kashyk, but the dilemma finally found some resolution with the introduction of another of Tom Paris' holodeck programs and the character of Michael Sullivan. In "Fair Haven" and "Spirit Folk" Janeway is finally able to let her hair down (in more ways than one), and the issue of fraternizing with her subordinates is happily laid to rest. This resolution however, was not without its detractors, including Kate Mulgrew herself.
"When I read that one, I went right over to (Rick) Berman's office and I said "What are you smoking?" I mean, how desperado is this broad!"
- - Kate Mulgrew (speaking at Sacremento, USA Convention 2003 (uploaded on YouTube))
Season six culminated in the assimilation of Janeway, Tuvok and Torres, as the crew again went head to head with the Borg Queen. This time, to assist an underground Borg Resistance threatened with annihilation.
- This is the first Star Trek season since TNG Season 6, in 1992, to premiere on its own. This coincided with the end of the seven-season run of Star Trek: Deep Space Nine in June 1999.
- Discounting season premieres/finales, this was the first season since season 2 not to feature a two-part/movie length episode during its run.
- "Barge of the Dead" featured Karen Austin as B'Elanna Torres' mother, one of the actresses apparently short-listed for the original role of Kathryn Janeway.
- "Survival Instinct" is the first time since "Living Witness" in Season 4 that Jeri Ryan appeared in a full Borg outfit.
- When asked what stood out about season six, Robert Beltran commented that he didn't have fun during this season, calling it "dreary and tedious" for him. 
- Characters which 'crossover' from other incarnations of Star Trek: Deanna Troi ("Pathfinder") and ("Life Line").
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