In no particular order, some of the moments that have led to debates among Star Trek fans: Sisko uses bioweapons against Maquis colonies - Deep Space Nine (S05E13) - "For the Uniform" - Sisko's actions are technically in keeping with previous continuity (i.e., the TOS episodes "Whom Gods Destroy" and "A Taste of Armageddon" state Starfleet General Order 24 allows a Starfleet captain to destroy all life on a planet if they deem the planet to be a threat to the Federation). And in justifying his actions to Eddington, Sisko says the Maquis bioweapons plus Eddington attacking a Federation starship has made the Maquis "an intolerable threat to the security of the Federation." On the other hand, if you stand back, think about it and try to mesh it with the quasi-utopian nature of the Federation, that's a scary amount of power to place in a captain's hands. Just imagine that a US Navy captain, on his own volition without orders, decided to use nerve gas against a group of Americans in Yemen or Pakistan whom the captain had decided were a threat to American security. There would be people calling that captain a human rights violator and want a prosecution. Janeway murders Tuvix - Voyager (S02E24) - "Tuvix" - Probably the most debated moment from all of Voyager is Janeway's decision to terminate Tuvix's existence after he was created by a transporter accident which merged Tuvok and Neelix. The argument generally boils down to two camps. On one side are people that argue Janeway corrected an accident, and was justified in her decision since she "saved" two members of her crew. On the other side are people who retort that no matter how Tuvix came into existence, he was a sentient being, she disregarded his choice to exist, dragged him to sick bay after he plead for his life in order to kill him. The fact The Doctor refuses to perform the procedure because of the ethics of it throws even more fuel on the fire of the controversy. Picard is willing to allow a planet's population to die - The Next Generation (S07E13) - "Homeward" - For people that dislike the Prime Directive, or at least dislike the TNG interpretation of it, they usually point to this episode where Starfleet and Picard are willing to allow an entire species to die out when their planet's atmosphere collapses rather than to help them survive and risk cultural contamination. Phlox convinces Archer that respecting evolution means letting a species die - Enterprise (S01E13) - "Dear Doctor" - Arguments about this episode usually revolve around the really bad understanding of how evolution works within the story (i.e., evolution doesn't strive towards a specific goal), with some finding its overall message "immoral." The fact that Archer and Phlox in the end do exactly what they claim to not want to do, play God by possibly condemning an entire species to a slow death based on their belief of what nature wants, doesn't exactly sit well since this episode is supposed to show the reasons why the Prime Directive was developed.