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That's a very common kind of questline, so with that being the only information to go on, it makes it hard to identify. Do you remember anything else about it? For example, was it set in modern times/the future/a fantasy world? What was the gameplay like? Every bit of information you can remember helps to narrow it down.
That said, it did make me think of a couple of games I recently played; one was called Frontier and the other was Hands of War. Was it one of those?
Edited by Syssareth
It was Hands of War, thanks for finding it.
This was a game I played last year. I remember that it was probably a flash game and that you played a soldier or something, and you could make alliances with a few different groups. You had to do things like killing enemy soldiers to be able to join the groups. I think one of the groups was a trading guild.