Where conventional wisdom suggests that Star Trek: The Next Generation (TNG) somehow depicted the darker iteration of Voyager during its second season or otherwise, the relationship between the two series is more a matter of common creative origin and tonal development than a strict on-air representation of the darker iteration idea.
The reality is in the concept of Voyager itself, which was originally conceived of as a far darker, grittier vision for the show than what the series eventually developed into.
Voyager's darkest early idea in Star Trek
When Voyager originally came into existence, the show was much darker than the squeaky-clean, light show that actually aired. The initial series pitch was for a Starfleet vessel stranded in the Delta Quadrant, far light-years from home and struggling to survive at every turn.
The series was intended to portray the crew of Voyager as constantly struggling to survive as the ship, increasingly, fell apart and disintegrated from all the damage it took as it relied on increasing amounts of alien and Borg technology for defense and repair. This "survivalist nightmare" would have been believable in a far grimmer and more desperate environment, since the Voyager of the era it came back was a battered and abused vessel.
The concept was that the crew would be increasingly resource-short, constantly struggling on dwindling supplies, and more isolated.
Switch to a more positive tone
Though the original dark concept, the direction of the series was altered before production. The showrunners did not end up following the dark, survival-oriented angle for Voyager but rather took on a tone more similar to TNG's—one of optimism, hope, and idealism. Consequently, Voyager was seen as a ship that was mostly in pristine condition, with damage and resource shortages downplayed in the interest of serial adventures.
Instead of the desperate struggle to survive, the series tended toward a more optimistic Star Trek tradition, less focused on desperation and decay and more on exploration and diplomacy.
Voyager, TNG, and DS9: A tone spectrum
In tone, Voyager stood between TNG's idealistic optimism and the darker, more serialized tone of Deep Space Nine. Though Voyager had a generally positive tone, it occasionally had darker material, as with such episodes as "Year of Hell" and "Dark Frontier," where stakes were much greater and the survival of the crew truly hung in the balance.
Yet it never quite committed to the darker side of its initial idea, nor did it hold onto the relentless dark tone of DS9. Deep Space Nine, with its prolonged wars and gray areas, pushed the dark aspects of Star Trek storytelling to their fullest extent, a tone Voyager never quite embraced, even at its darkest moments.
Some of the notable darker episodes in Voyager
Although Voyager never embraced the dark tone in its entirety, some episodes did lean towards the darker, grittier storytelling that was part of its original concept.
Most significantly, "Year of Hell", a two-part Season 4 episode, looks at the scenario in which Voyager is under constant attack, taking massive damage and pushing the crew to the breaking point. The episode is closest to the realization of the dark vision for Voyager, with the ship in distress and the crew having enormous physical and moral difficulties.
Likewise, "Dark Frontier" during Season 5 explores the Borg threat more deeply, and the crew embarks upon a multilayered heist of immense moral complexity in exchange for being accepted into the Borg Collective. The episode is on the cusp of extending its happier Voyager tone to this one as it delves into the grayer extremes of Borg assimilation, identity, and self-sacrifice. It is the only show where Voyager's psychological and moral stakes are approximately on par with those of DS9.
Finally, although Star Trek: The Next Generation never had a different, darker version of Voyager once or during Season 2, the initial development of the show did incorporate many more dark possibilities for the series.
The final Voyager that was created was more on the optimistic side of TNG, with an occasional dip into darkness. Episodes such as "Year of Hell" and "Dark Frontier" represent Voyager's best efforts at experimenting with the grittier, survivalist idea that had been created early in production.
The early "dark Voyager" was not something that appeared in TNG's narrative but more of a behind-the-scenes concept that eventually influenced the show. What was on TV for the Voyager fans was more utopian and light, but there are remnants of the original in some episodes where there were stakes and the crew's survival was really at stake.
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