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At the end of the Star Trek: Voyager pilot "Caretaker", Janeway informs everyone that she and Chakotay (leader of the Maquis crew) have agreed to integrate as a wholly Starfleet crew.

Both crews are going to have to work together if we're to survive. That's why Commander Chakotay and I have agreed that this should be one crew. A Starfleet crew. And as the only Starfleet vessel assigned to the Delta Quadrant, we'll continue to follow our directive to seek out new worlds and explore space.

I get that Chakotay would agree with Janeway that one crew working together increases their chances of survival. But what I don't get is why Chakotay is willing to do so as "a Starfleet crew" and all that entails (most notably, wearing Starfleet uniforms and strictly adhering to the Prime Directive). Very few of the Maquis are Starfleet graduates, and as we see in the next episode, two of the Maquis tell Chakotay they're willing to support a mutiny in order to bring about a Maquis-style of leadership.

Why does Chakotay agree to a full Starfleet-style of leadership instead of some sort of hybrid crew that uses aspects of both Maquis and Starfleet protocol as they see fit? That would seem like something that would reduce the amount of tension from the Maquis, and would mean that Chakotay wouldn't be bound to enforce Starfleet command decisions if Janeway were killed and he became the senior officer.

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    I don't recall but perhaps you do: What was the ratio of Starfleet to Maquis personnel on the ship at the time? Janeway was pretty strict about adhering to her ethics IIRC; if she also had the numbers it may have been a "my way or the highway" kind of agreement. – Steve-O Jul 3 at 1:25
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    I lean towards Seska's judgment of Chakotay, i.e. a fool following a fool, but really Voyager was the only game in town. It's not like Janeway was going to equip him for his own military campaign and let the Maquis carve out their own little empire in the Delta quadrant. – Kyle Jones Jul 3 at 4:11
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    @HarryJohnston End of episode 2: CHAKOTAY: Can I ask you a question, off the record? If things had happened differently, and we were on the Maquis ship now instead of Voyager, would you have served under me? JANEWAY: One of the nice things about being Captain is that you can keep some things to yourself. I get that determines who is in charge, but it’s unclear to me why that means 100% Starfleet, uniforms and all. – Thunderforge Jul 3 at 4:12
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    @KyleJones Sure, the Maquis never intended to settle in the Delta Quadrant. But why not say “Sure, we’ll serve as one crew, but we’d rather not have to wear the Starfleet uniforms, and we’ll have to have a long talk about why we don’t want to follow the Prime Directive and want to use some Maquis training tactics.” – Thunderforge Jul 3 at 4:17
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    You may wish to note that once the Cardassian joined the Dominion, most surviving Maquis members were pardoned and many joined (and captained) Starfleet vessels. – Valorum Jul 3 at 7:44
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This is addressed in the show's 'bible', a guide for prospective writers to give them some background into the series before submitting scripts. In short, both captains recognised that it would be in their best interests to combine their crews. Chakotay negotiates key positions for the Maquis (notably First Officer for himself) and a general amnesty and in return, Janeway seems to have agreed to do so on the condition that the crews maintain Starfleet order, including taking commissions. Since both parties get something-for-something, Chakotay strikes the deal and they combine under a Starfleet banner.

They also find the Maquis ship there, and, in an uneasy liaison, the crews of the two ships agree to band together in order to maximise their chances of surviving and returning to Federation space.

But the Maquis ship is destroyed and and its crew must come aboard Voyager. The two ships' captains negotiate for key positions: The Maquis insist on certain pivotal roles for their senior staff. An agreement is stuck, and the ship sets out, manned by this unusual mix of Starfleet and renegade officers - - some of whom get along, and some of whom don't

VOY: Show Bible

He then leverages this agreement (and his own position) to secure key roles for his former officers.

JANEWAY: Okay. The personnel situation. We've managed to find a replacement for the Transporter Chief, but we still need an Astrogation plotter, a Chief Engineer, medical support personnel.

CHAKOTAY: I've made a list of several Maquis crew members who would make good officers.

VOY: Parallax

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