If you're talking before season 4 then 100% she sides with Chakotay. Her loyalty to him runs deep. I think even after that she will side with him but would be more conflicted because likely Tom will side with Janeway.
In "Voyager's Conspiracy" (6x09), although she seemed conflicted, she eventually ended to side Chakotay, at the expense of - her well installed (romantic) relationshipship withTom Paris (a contrario, you can be sure that despite being in love with B'Elena, Tom Paris would have refused to blindly follow her siding especially with Chakotay, in particular if its was against Janeway) and - her friendship with Janeway, who she even goes to consider as a (second) mother. In any case, someone who has been there for her, encouraging and supporting her when others.doubted her good intentions and loyalty but maybe they were right to do so, when we see her! I strongly believe in friendship and loyalty but IMHO, here, Torres decision to side Chakotay at this moment of their journey, was not only unwise but unfair to Paris & Janeway too, especially after what she has got from them: love and trust.
Oops, comment continued: In short, it would have been more reasonnable on her part to answer Chakotay's request/order not to do what Janeway has ordered and to pursue her activities, while responding to Chakotay something like "Sorry Chakotay, I don't know what happened/happens between you and Janeway but I I'm having no part of it. Resolve your problem and make it fast". Hey soometimes, even Chakotay needs to be put in his place by one of his friend. ;-)
I would actually love to see this. I think she may side with Chakotay but she certainly might go with Tom and Janeway. But what if Tom also joins Chakotay? She would also be going against Harry who will for sure side with Janeway
This basically what happens in that season 3 last episode. Torres reluctantly goes along with Chakotay in the "mutiny holonovel" Paris pretends to join him, then betrays him to help Janeway.
Imo Chakotay and B'Elanna went through something with the Maquis that formed a permanent, unbreakable bond. It is strongly illustrated in Extreme Risk. She says the Maquis were her family and they were fighting for a cause she and Chakotay truly believed in. She almost self destructs when she loses them. Chakotay is the one to step forward and confront her about the self harming behavior, not Tom or Janeway. He says they will work on it together and only leaves when she says she is OK. This makes a lot of sense to me because under combat your life depends on these bonds. They are created in extremely hazardous combat situations and, forged under fire, they are often unshakable. Brother's in arms. It is why betrayal by someone within such a close group is so overwhelming. It's why Chakotay does what he did in Manoveurs. The betrayal cuts that deep. I believe this is why she sides with Chakotay in the Voyager Conspiracy. In Life Line, Chakotay reminds Janeway she may have forgotten he, B'Elanna and others were Maquis but they have not. The bonds are just that strong.
What let me think that Janeway was wrong to trust them by giving them key positions aboard (in particular to Chakotay & B'Elena Torres or even Alaya, to a lesser extent). Renegades some days, always renegades, as the saying goes! As for the confidence/protection/loyalty Janeway brought them during the journey when Starfleet's admirals surely questionned her about their loyalty to the organization (and just as surely, will continue to bring them, once back on Earth to avoid their confinement in federal prisons and ensure them a general pardon in rapport relevant from their past (and crriminal) activities in the Maquis) were always been one way.
I totally agree. The Maquis are a long way away and the ideology they fought for is in the Alpha Quadrant, not the Delta. It is also over. Chakotay and B'Elanna are not Sudar. They fought for the cause which is dead. I also think they proved their loyalty 1000 times over. If there was any chance Chakotay would lead a mutiny in later seasons it was Equinox and the Starfleet crew just might have followed him but he did not. Even Janeway herself acknowledges it.
Well we dont' have as much backstory on him but he was a Starfleet officer. On Voyager he falls right back into that way of thinking. I was listening to a podcast the other day and they kind of had a good point about why the maquis and starfleet people meshed so quickly. The maquis were more against the cardassians than the federation. Remember in Drednaught B'elanna programmed it to warn off federation ships. The maquis were fighting to protect their homes and many of them were former starfleet people. In the Delta Quadrant they're out of the fight. They have no real reason to maintain the Maquis attitude so they fall back to their initial Starfleet training.
Early in the series, Chakotay. Later, she probably comes to the conclusion Ckakotay is under some kind of alien influence and isn't himself. Chakotay was rational enough that the only way he would have ever mutinied is if Starfleet treated them unfairly or if they did something as bad as the Equinox crew did.
Torres never sides with Janeway against Chakotay, but I think after the first season or two, if Chakotay tried to lead a mutiny Torres would come to the conclusion he was under alien influence because she knows him well enough to know he wouldn't rebel against Janeway.
I think that in the later seasons it would take Janeway vastly over stepping her bounds or maybe being under alien influence or something-the Equinox incident times 10 or something. In seasons 1-3 she would support Chakotay I think pretty reliably unless she had good reason to believe Chakotay was either not himself or under some sort of manipulation. In seasons 4-5 I could see her wavering somewhat. By season 6 though I don't think it likely she would participate in a mutiny unless the situation was very bad.