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I understand that you can only play as the Federation or Klingon. Setting the Klingon thing to the side for a moment, is everyone who plays as Federation IN the Federation as a Starfeet guy or can you be sort of freelance civilian?
Does it work like that?
Above all else... never ever piss off the penguin.
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It's been a minute since I last played, but I believe everyone is in Starfleet. Though not all ships are federation ships. From what I remember you can get Ferengi ships (for example) out of lockboxes.
This being the main focus of the developers these days.
As time goes it on, this game seems to be more and more coercive in regards to making people buy lockbox keys or make C-store purchases.
And less about making the game "better".
Cryptic has like many MMO devs made many promises over the years and fulfilled all too few.
We can only hope the license for this game is not renewed and the next ST MMO will be better.
As others have stated, "no" and it's not like you can go rogue on Starfleet. You can't join the Marquis and fight Feds or abandon technology and form your own colony. STO is a superficial game. There are no options for freelancing.
2 factions ! Hahahaha ! Try 1 and 2/5 th's . Even that may be and exageration. They gave up on Klingon faction about season 3 or 4 . So you're basically confined to a very linear one faction game, going to Klingon perhaps to harvest a bit more since the new season was introduced.