Ever since its creation in the late 1960s, Star Trek has been very good at presenting the often blurred line between good and evil. The show tackles deep and complex philosophical questions, as well pushing topical and often political issues into the limelight through its allegorical science fiction storytelling. The show's protagonists are often thrown into situations with impossible odds, forcing them to make hard decisions all under the notion of doing so for the greater good.
These instances are almost always justifiable, and audiences usually agree with the logic and reasoning behind these apparent immoral or unethical acts. However, there have been a few moments in Star Trek history where characters have crossed the line. In fact, each and every Captain protagonist is guilty. While all of them have done bad things, here are the franchise's top three culprits.
Janeway
Captain Kathryn Janeway from the show Voyager is potentially the most egregious example of a Star Trek captain going too far. The show has received a lot of hate over the years, and a lot of this is directed at the morally devoid choices made by Janeway, all under the facade of doing so for the greater good. She is guilty of the downright murder of Tuvix, as well as assisting the Borg in the Genocide of species 8472. However, something that hasn't been discussed as much is the blatant use of torture to gain information in the season 5 episode “Equinox.”
Here, the USS Voyager, in their long journey home, comes across another Starfleet ship stranded in the depths of space. Everything starts off well, but it’s soon discovered that their Captain, Rudolph “Rudy” Ransom (his real name, believe it or not), has been using extra-dimensional space creatures as fuel to improve their warp capabilities and get home faster, killing these sentient beings in the process. Upon discovering this, and following a short firefight between their two ships, Janeway captures a member of Ransom's crew. She proceeds to literally torture him by exposing him to the space creatures, all to gather more information on his captain.
Picard
While normally seen as one of the more moral abiding and just captains of the franchise, Jean-Luc Picard is no stranger to getting his hands dirty when the need arose. While most of these instances were based on logical outcomes and justifiable risk, there is one instance where he took things too far, and recklessly endangered the entire Federation when a perfectly logical alternative was presented to him.
The moment in question comes in the movie First Contact, where the cybernetic body-snatcher Borg manag to find a way to travel back in time, hell-bent on assimilating earth before the Federation could be formed. Picard and his crew follow, and manage to destroy the Borg cube, but not before some of them infiltrate his ship. With no chance of aid, trapped in a different time, there is no chance of being rescued. Worf tells the captain that their only option is to self-destruct the ship and kill all Borg onboard, stopping them from taking over the ship and continuing with their time-altering mission.
Blinded by his rage towards his nemesis, Picard refuses. Though he is normally so trigger-happy with the self-destruct sequence, he chooses instead to fight them himself. What follows are some pretty cool John McClane-esque moments, but he is stopped abruptly when he comes across a civilian, who makes him realize he has almost single-handedly guaranteed Borg victory. It is one of the few times that Picard's judgment is clouded with his anger, an emotional decision that halted all reason.
Sisko
Like Janeway, Sisko’s name often brings mixed feelings of morality for fans. The only difference was that while Voyager chose to sweep these moments under the rug and never address the terrible things Janeway does, Deep Space 9 focuses pretty heavily on his. The theme of saving the universe at the cost of one man’s conscience is present throughout the storyline. The captain took some extreme actions during the events of the Dominion War and the franchise-changing episode “In The Pale Moonlight.” These actions, while still bad, were the results of a trapped man who had been backed into a corner.
A better example of crossing the line for unnecessary reasons comes with Sisko’s hunt for his former Security Chief, a man named Michael Eddington who had defected to the Marquis. They had been fighting the Cardassians and their methods had become increasingly aggressive, with Eddington having begun using biological warfare to remove Cardassians for their occupied homes. Sisko, angered by this, decides to turn the table and use Eddington's methods against him. He attacks a Marquis colony with Trilithium resin, a poison that is not only deadly to most species, but makes the entire planet uninhabitable for many years. His attack results in Eddington outlawing the use of biological weaponry and turning himself in. This ends up saving countless lives, but does not justify Sisko’s methods. The moment has been somewhat brushed under the rug, with it being suggested all the Marquis managed to evacuate before getting killed. However, it is still an unforgivable attack that was utterly avoidable.
These examples are not perhaps the most obvious examples of these protagonists crossing the line for the greater good, but they are the most avoidable. Each one of them has done these reprehensible things for what they believed would be for the best in the bigger picture, despite a plethora of other options less that were less morally ambiguous. One honorable mention goes to Archer of Enterprise, who steals an innocent ship's warp coil and abandons them to go and save earth from a Xindi super weapon. Another goes to Kirk, who steals the iconic USS Enterprise from Starfleet, and disables a fellow (admittedly incompetent) captain's ship to stop pursuit, all to go and resurrect Spock.