Caretaker, Parts I and II
During the crew's first mission, Janeway makes the critical decision to destroy the Caretaker's Array — and with it, the crew's one shot at getting home. In doing this, she saves the Ocampa and makes a mortal enemy of the Kazon. It can be argued that her decision goes against the grain of the Prime Directive — after all, Janeway firmly takes a stance in a conflict between two species, taking action that alters what otherwise would have been an inevitable outcome. As Janeway points out, however, Voyager was inextricably involved in the situation long before she actually had to make her decision. Also, as the Kazon try to forcibly obtain Voyager's technology, perhaps this could be seen as Janeway's first attempt at bending the Prime Directive in order to survive in the Delta Quadrant.

Time and Again
Here, Janeway and Tom Paris are sent back in time, and must decide whether to warn the residents of a planet of a devastating explosion that is about to occur. Though Janeway initially warns Paris against violating the Prime Directive by revealing what they know, she changes her mind when she discovers that the explosion was actually caused by Voyager, and seeks to undo the damage. It can be argued that she is actually attempting to uphold the Prime Directive by negating Voyager's involvement in a planet's development — or in this case, destruction. Any further debate of this particular incident leads to larger issues of timeline distortion and its consequences.

Prime Factors
In this instance, the shoe is on the other foot. The crew encounters the Sikarians, a race possessing technology that could send Voyager 40,000 light years closer to home. The Sikarians, however, have their own Prime Directive — a law that prevents them from sharing technology with less advanced species. Several crewmembers conspire to obtain the technology through less than ethical means, but their efforts are in vain — the technology is incompatible with Voyager. Janeway takes a firm stance as far as the Prime Directive goes here, knowing that it wouldn't be consistent with Starfleet's own policies to obtain the technology unethically.

Prototype
A race of sentient robots forces B'Elanna Torres to construct a prototype power module so that they may build additional units. She later learns, however, that this unit will allow the robots to win their war against another group of robots. In the beginning, Torres wants to build the prototype, but Janeway rightly points out that the Prime Directive prohibits such action. Later, the robots capture Torres and threaten to destroy Voyager if she doesn't help them. She does, but when Torres learns of the prototype's purpose, she destroys it, despite the possible destruction of her ship. Both Janeway and Torres follow through in upholding the Prime Directive — even though Torres, in particular, knows that her actions may lead to devastating consequences for Voyager.

Scorpion, Parts I and II
When Voyager gets stuck in the middle of a conflict between the Borg and Species 8472, Janeway faces a terrible decision: retreat farther from home or face the Borg and be assimilated. In the end, she comes up with an alternative: aid the Borg in developing a weapon to defeat Species 8472, in exchange for safe passage through Borg space. While the Borg are obviously more advanced than many of the civilizations the Prime Directive often applies to, there's no denying that Janeway's interference here — and the knowledge she supplies the Borg with — decisively alters the outcome of a major conflict. This situation, however, is influenced by the special circumstances surrounding Voyager's presence in the Delta Quadrant. As there is no Starfleet or Federation close by, Janeway's decision hinges mostly on survival, and keeping her crew alive in this deadly region of space.

The Killing Game, Parts I and II
Hirogen hunters take over Voyager and use the holodeck to recreate World War II, with the crew as their unsuspecting prey. In the end, Janeway offers the Hirogen holodeck technology in exchange for the return of her ship. While the Hirogen are warp-capable, holodeck technology will have a major effect on their society — it might be a positive one, but it will undoubtedly alter the course of their evolution as a species. One could argue that Janeway is again merely trying to survive, to get her ship back and keep the crew safe by any means necessary. Still, as Janeway has proved that she is quite capable of coming up with alternatives to tough decisions in the past, perhaps she could have applied more creative thinking here, so as not to commit so blatant a violation.

Demon
A mysterious metallic compound on a "demon" planet experiences awareness for the first time when it creates doubles of Voyager crewmembers. In the end, the crew donates DNA samples so that the planet can populate itself. There isn't much of a justification for this violation, as it interferes with a civilization that not only lacks warp capabilities, but hasn't yet evolved to actual sentience. Not only that, but the population of the planet has all the memories of the Voyager crew, which could have repercussions for this region of space.

Equinox, Parts I and II
The crew encounters another Federation ship in the Delta Quadrant — Equinox, commanded by Captain Ransom. Janeway learns that Ransom and his crew have been using nucleogenic lifeforms to enhance the ship's propulsion systems, hoping to increase their chances of getting home quickly. In doing so, they are killing these lifeforms. Though Janeway is eager to get back to the Alpha Quadrant, she recognizes that this particular method not only violates the Prime Directive, but nearly everything the Federation stands for. In taking decisive action against Ransom and his crew, Janeway reaffirms Voyager's commitment to the Prime Directive — and hopefully, gets a glimpse at what could happen if she were to bend the rules too far in order to get home.

Dragon's Teeth
Here, it is Seven of Nine who initially interferes with an outside species, but Janeway also contributes. When the crew discovers an underground chamber with lifeforms in stasis, Seven activates one of the pods without Janeway's permission. She awakens Gedrin, one of the Vaadwaur, a race that had developed subspace corridors for exploration. They put themselves into stasis when they were attacked. Janeway agrees to help Gedrin and his people fight against their enemies in exchange for passage through the subspace corridors ... and Voyager essentially involves itself in a conflict by allying with one species over another. Perhaps Janeway is merely trying to find the fastest way home possible, but it is at the expense of the Prime Directive.

Memorial
Voyager encounters a structure that is sending neurogenic pulses throughout the surrounding system, so that anyone who enters experiences memories of a centuries-old battle. The crew of Voyager experiences fragmented versions of these memories, as the structure's power cells are deteriorating. Janeway insists her crew recharge the power cells, so that the memorial will continue to spread its message. This is a tricky one — the civilization in question is already gone, its fate decided. Still, it would seem that charging up the power cells of a dying memorial is a decision based more on Janeway's personal beliefs than Starfleet's policy of non-interference. Though captains must face moral quandaries all the time, they usually look to the Prime Directive to guide them.

Natural Law
When Seven and Chakotay are stranded on a planet, they encounter a primitive race of people. Later, they learn that these people, the Ventu, are surrounded by an energy barrier erected centuries earlier to protect the Ventu from the other species on the planet, the Ledosians. When Voyager penetrates the barrier in order to rescue their people, it looks as if the Ventu culture will be influenced by the Ledosians. Thus, Janeway decides to re-establish the barrier, preserving the Ventu culture as it is. The major point of contention here is that the Ventu have already been culturally contaminated by their interaction with Chakotay and Seven — some of the men paint Chakotay-like tattoos on their foreheads, while a woman straps a piece of shuttlecraft to her head in order to emulate Seven. While it can be argued that first contact with the Ventu was unavoidable, part of the Prime Directive mandates that crewmembers are considered expendable in order to prevent such a violation. Janeway's decision to re-establish the barrier seems to indicate that she wishes to preserve the Prime Directive and keep the Ventu from being interfered with, but Voyager already has interfered. Also, Seven notes that the Ledosians may have scanned Voyager's technology, and might be able to figure out how to remove the barrier themselves. Whatever may happen in the future, it is impossible to argue that Voyager's involvement here won't have consequences for this society in the years to come.

Overall, Janeway and her crew did their best to uphold Starfleet's policies, but occasionally, they had to resort to unorthodox methods of problem-solving. Some of these methods can be interpreted as violations of the Prime Directive. All of these experiences resulted in valuable lessons for the crew, however — lessons which will hopefully aid them when they encounter issues involving Starfleet's most sacred law in the future.

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