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Has force ever used to make a planet join/stay within the Federation?
I know the Federation did not overtly go out invading or overthrowing governments, but, especially in the early days did it help populaces overthrow tyrants, defend itself from empires fighting against it, with the resulting win leading to those planets choosing to join? Or did every planet willingly just become part of the federation and accept its rules and laws?
That's a big yes. While always well intentioned, the original Enterprise crew used force to achieve their goals on more than one occasion. It's important to note that the mission of the NX-01 is what ultimately led to first contact and eventually cooperation with a handful of alien races that would ultimately lay the groundwork for the United Federation of Planets as confirmed by a conversation with the time traveler Daniels in ENT: "Shockwave" and corroborated by information obtained from a computer aboard the USS Defiant in ENT: "In a Mirror, Darkly".
There are at least 2 instances of the original Enterprise crew using force to accomplish their goals (which ultimately lead to the founding of the Federation). The first being the destruction of an unarmed Xindi communication center near where the Xindi weapons system was being tested in ENT: Azati Prime. This led to the deaths of 2 Xindi working at the facility who presumably would have alerted the Xindi high command once their orbit had brought them back info communications range. The second notable incident occurred in the very next episode in which Captain Archer forcibly takes a warp coil from a ship of Illyrians who are unaffiliated with either side of the Xindi conflict and seem to be peaceful. Archer first attempts a peaceful negotiation to obtain the warp coil he desperately needs, but the Illyrian captain refuses saying that without the part the Illyrians would be stranded 3 years from home with no way to defend themselves. Archer deliberates over his limited options before leading an armed boarding party to retrieve the warp coil stunning numerous Illyrians and damaging their power grid in the process.
Your question says "ever". If you mean "in the early days", feel to revise your question.
Sisko's primary mandate as commander of DS9 is to help Bajor become ready for membership in the Federation. He repeatedly uses force to accomplish that goal.
In the pilot of DS9, Sisko is given broad authority to ensure Bajor's eventual membership in the Federation.
SISKO: Sounds like they're not ready.
PICARD: You must do everything short of violating the Prime Directive to make sure that they are.
Throughout the series, we see Sisko use force against the Cardassians, Bajoran terrorist factions, and even the Bajoran government itself, all in an attempt to follow those orders.
