Star Trek: Voyager’s 7 Biggest Janeway & Chakotay Feuds, Ranked Worst To Best

Despite a close relationship on Star Trek: Voyager, Captain Janeway (Kate Mulgrew) and Commander Chakotay (Robert Beltran) had some intense feuds during the show's seven seasons. Janeway and Chakotay are one of the most interesting command teams in the Star Trek timeline. The two started as fairly cut-and-dry enemies when Janeway was sent to track down Chakotay's Maquis ship after it disappeared in the Badlands. However, after both her and Chakotay's crews became stranded in the Delta Quadrant in Voyager's pilot episode, "Caretaker," Janeway and Chakotay agreed to combine their resources and work together to get home.

After Chakotay's crew became part of Voyager's cast of characters, Janeway and Chakotay embarked on building an intense friendship that was sometimes charged with romantic chemistry. Despite never becoming a couple on Voyager, the two shared an intimacy that most other Star Trek command teams did not, and this was evident in numerous episodes of the series. Janeway and Chakotay generally worked well together, eventually navigating their ship and crew to safety back in the Alpha Quadrant by the end of Voyager's run, but there were also numerous times when they didn't get along.

7 Alliances

Season 2, episode 14

"Alliances" was one of the earliest Voyager episodes that depicted a real conflict between Janeway and Chakotay, but ultimately the feud was contained to a single episode and had little impact on the show as a whole. During the episode, Janeway and Chakotay engaged in an argument over whether to attempt an alliance with the Kazon, who had been terrorizing the ship since Voyager season 1. In actuality, the fight between Janeway and Chakotay boiled down to whether or not to adopt more Maquis principles and tactics to survive in the Delta Quadrant against things like that Kazon's attacks.

While the discussion of Starfleet vs. Maquis issues was interesting, this feud was so short-lived that it's almost completely forgettable in the grand scheme of Voyager's timeline. The fact that the episode heavily involved the Kazon also didn't help the popularity of Janeway and Chakotay's argument. The Kazon were a universally hated Voyager villain, and most of their storylines ended up being ones that audiences would rather forget. Ultimately, although an interesting microcosm of some larger issues in Voyager's first two seasons, "Alliances" didn't contain a particularly juicy Janeway and Chakotay feud.

6 Parallax

Season 1, episode 3

Aside from their minimal conflict in Voyager's pilot episode, the first real fight between Janeway and Chakotay happened in episode 2, "Parallax," over the question of who would become the ship's Chief Engineer. The feud centered around whether it was a good idea to promote the former Maquis B'Elanna Torres (Roxann Dawson) to Chief Engineer over the Starfleet Lieutenant Carey (Josh Clark). While Janeway was on Carey's side initially, she ended up getting persuaded by B'Elanna's actions during the episode and Chakotay's argument.

Although the conflict over B'Elanna in "Parallax" was great at establishing Voyager's character dynamics, it was also fairly short-lived, not progressing much beyond one episode. The conflict was also understandable since Janeway was still feeling her way into trusting Chakotay and his crew, and the argument ended by showing that she could rely on his judgment. The issues at stake were more interesting than "Alliances," but the outcome was fairly predictable and easily forgotten about once everything was resolved.

5 Year Of Hell, Parts 1 & 2

Season 4, episodes 8 & 9

Often considered one of Voyager's best two-part episodes, "Year of Hell, Parts 1 & 2" also contained a more nuanced conflict between Janeway and Chakotay. As the result of a series of devastating attacks by Annorax (Kurwood Smith) of the Krenim Imperium, the USS Voyager was severely damaged, with the crew suffering multiple injuries. Over the course of several months, Annorax's attacks progressed, further destroying the ship. Throughout this, there was tension between Janeway and Chakotay about whether to abandon the ship to save the crew or stay and keep fighting.

Despite the caliber of "Year of Hell" as an episode, Janeway and Chakotay's conflict in the storyline was surprisingly short-lived, and even before it ended, never particularly heated. It was clear that Chakotay was firmly on the side of abandoning ship during the episode, but he kept his opinions mostly to himself and instead generally worked to keep Janeway from losing her humanity during her relentless fight against Annorax's attacks. Chakotay was also captured by the Krenim at the end of the episode's Part 1, effectively ending any more direct contact with Janeway.

4 The Voyager Conspiracy

Season 6, episode 9

A highly amusing episode, "The Voyager Conspiracy" provided one of the few times Janeway and Chakotay were tricked into a feud rather than naturally finding one between themselves. In this case, Seven of Nine's (Jeri Ryan) paranoid behavior after a botched assimilation of a massive amount of the ship's data caused Janeway and Chakotay to suspect each other of plotting behind the other's back. In reality, Seven essentially pitted the two against each other needlessly, which Janeway and Chakotay discovered only after a suspicion-laced conversation.

Although their conflict in "The Voyager Conspiracy" was manufactured, Janeway and Chakotay's confusion and suspicion of each other during the episode was truly fun to watch. Seven's ability to effectively set them at odds was quite hilarious, and a case of misunderstanding or misinterpretation always makes for good conflict. On the flip side, the end of the episode reaffirmed Janeway and Chakotay's friendship during a scene where they agree to never stop trusting each other again. Even though the conflict went no further, the complete arc of it was satisfying.

3 Night

Season 5, episode 1

"Night" contained one of the more emotionally intense feuds between Janeway and Chakotay, mostly because it surrounded Janeway's mental health. The episode kicked off season 5 with a storyline that saw Voyager's crew traveling through a completely starless region of space. This had numerous psychological effects on the crew, most of all Janeway who fell into a deep depression. Throughout the episode, she continually butted heads with Chakotay over whether she was still fit to run the ship, stubbornly refusing to come out of her quarters until the episode's conflict forced her back out into the open.

It should be noted that Janeway and Chakotay's conflict in "Night" was not the result of any failing on either part, but rather Janeway's deteriorated mental health causing her to be too hard on herself. Still, the tension between Janeway and Chakotay during the episode was genuinely dramatic and made for some powerful scenes, culminating in Chakotay needing to talk Janeway down from going on essentially a suicide mission with the rest of the crew's help. "Night" revealed a lot about Janeway and Chakotay's characters and how their relationship was faring roughly five years into their journey home.

2 Scorpion, Parts 1 & 2

Season 3, episode 26, and season 4, episode 1

When considering episodes with Janeway and Chakotay feuds during Voyager's run, "Scorpion Parts 1 & 2" stand out above the rest. The episodes themselves reached new heights for Voyager, featuring the introduction of Species 8472 and acting as the start of the show's substantial Borg plotline thanks to the first appearance of Seven of Nine. However, amid all the chaos of Voyager's first foray into Borg space, "Scorpion" was at heart a reexamination of Janeway and Chakotay's relationship, pushing their trust in each other to the limit.

"Scorpion's" main source of the conflict was Janeway's desire to ally with the Borg, something no other Starfleet crew had accomplished. Although the beginning reaffirmed how much Janeway relied on Chakotay, his clear dislike of her plan led to a massive rift between the two by the end of Part 1. In Part 2, things devolved even further when Chakotay broke his promise to uphold the alliance during his command of the ship when Janeway was injured. "Scorpion" showed the first major breach of trust between the two characters, and introduced more complex dynamics into their relationship.

1 Equinox, Parts 1 & 2

Season 5, episode 26, and season 6, episode 1

Of all the feuds that Janeway and Chakotay had throughout Voyager, the one in "Equinox Parts 1 & 2" was unequivocally the best, most intense fight the two ever engaged in. The episode is another strong two-parter, revolving around Voyager's crew encountering another Starfleet ship in the Delta Quadrant, the USS Equinox. When it became clear that the Equinox crew had heavily compromised their principles by slaughtering an alien species to use as fuel to get them home faster, Captain Janeway began a relentless pursuit to try and bring them to justice.

While Chakotay didn't agree with what the Equinox crew had done, it was Janeway's brutal tactics that led to conflict between the two. In fact, Chakotay nearly committed mutiny against Janeway after she almost killed an Equinox crew member while torturing him for information. Things got so bad that Janeway briefly removed Chakotay from command, and although the conflict was resolved, their relationship was left more shaken than it had ever been. Out of all the feuds between Janeway and Chakotay in Star Trek: Voyager, it is the most surprising that they ever recovered from the events of "Equinox."