Summary
One of the core tenets of theStar Trekuniverse is the Prime Directive, a strict rule that must never be broken. Considering the social and career-related consequences of violating the Prime Directive, that doesn’t stop Starfleet Captains from finding excuses to break it all the time.
Ask Captain Janeway if she’s ever broken the Prime Directive, and her answer would be a not-very definitive “no” followed by a very long-phrase starting with “except.” The exact question she was asked in theStar Trek: Voyagerepisode “Equinox” was not if shehad, but howmanytimes. Given that the theme ofVoyagerwas one of survival as opposed to exploration, it might be unfair to judge Captain Janeway on the same metric.

1The Killing Game
The Hirogen And The Holodeck
The Hirogen were a nomadic race of hunters that wandered throughout the Delta Quadrant in search of prey. They came across Voyager a few times,and this episodewasn’t their first encounter, but it was their most successful.
The Hirogen were able to use the Holodeck to deceive or brainwash the crew into thinking the simulations they were in were the real thing, and Janeway had to find a way to retake the ship. Although the Hirogen were technologically advanced enough to travel through space at warp speed, their evolution had stagnated.

Part of Janeway’s rationale forgiving them the holodeck technologywas not only a way to save the ship and crew, but also a way to prompt further evolution. This argument convinced the Hirogen, but that still doesn’t change the fact that giving them this tech was a violation of the Prime Directive.
2Equinox
Was It Justice Or Revenge?
“Equinox” was a two-part episode that spanned the gap between Seasons 5 and 6, with the introduction of the Equinox and Captain Ransom taking up most of the first episode. It wasn’t until the second episode, after Ransom betrayed Janeway and the Voyager crew, that things started to get ugly.
Janeway wasn’t only after Ransom because he had betrayed the basic tenets of everything the Federation stood for, but also because he had led them on and always planned to sacrifice them to ensure his survival. Among the many unethical things she does to catch him and keep him from killing more aliens to hasten his journey home, one of them is interfering with another race, the Ankari.

The Ankari understood warp technology, but they were a simple and peaceful race,and Janeway used her powerto coerce them into cooperating. Ransom had broken the Prime Directive in dealing with them in the first place, so when Janeway forced them to help capture him, it could be seen as two wrongs making a right.
3False Profits
Righting A Greater Wrong
Sometimes, you have to break the Prime Directive to clean up a mess that someone made when they broke it first. That’s one way to summarize the plot of “False Profits,” which has a backstory that goes back to one ofThe Next Generationepisodes, “The Price.”
While investigating a possible wormhole that can shortcut themback to the Alpha Quadrant, Voyager discovered a nearby planet with Bronze-age level technology that also has replicators. It turns out that two Ferengi had gone through the wormhole from the Alpha Quadrant years ago, but couldn’t get back. Instead, they settled on the nearby planet and made a cozy life for themselves pretending to be demigods.

Janeway decides to correct this mistake by creating her own “false prophet” or in this case Neelix in disguise, to convince the population that it was time for their “gods” to be on their way. The Ferengi are then removed from the planet but stay around long enough to steal a shuttlecraft and get through the wormhole again, only to collapse it and leave Voyager behind.
4Scorpion
Humans Co-Operating With Borg
The Delta Quadrant was a dangerous place partly because of the Borg, and Janeway couldn’t always dodge them. In the two-part episode “Scorpion,” Janeway agreed to swap some tech knowledge with the Borg, a clear violation of the Prime Directive. The idea was to give Voyager an edge in their journey and help the Borg fight against Species 8472.
Of course, the story’s moral is that Borg can’t be trusted, and Janeway knew that and planned for it. When the Borg, through Seven of Nine, tries to betray Voyager and take over, the crew uses a neural relay to zap Seven into submission and escape.

This could be Janeway’s most egregious violation of the Prime Directive, but there’s one other involving the Borg that might be even worse, so it’s a good thing it never actually happened.
5Endgame
The Developing Civilization Was Us
This is another time that Janeway made a deal with the Borg, but that’s not the point where she violates the Prime Directive. The knowledge and tech are only partly for them, but it’s really for her younger self and the other crew members.
It took Voyager 27 years to get home,according to the original lore, and looking back on her life Admiral Janeway decided there was a way to do better. She travelled back in time a hatched a plot that involved her younger self and a network of Borg wormholes that Voyager could use to get home in only seven years. The plan worked, Admiral Janeway was killed in the ensuing destruction, and Voyager made it home.

With the timeline changed, this sequence of events was erased. So the one time that fans can say Janeway clearly and deliberately broke the Prime Directive, it never actually happened anyway.