With the Earth used up, humans had to find a new solar system to call our own. We found one we liked, and forced it to sustain us all. The central planets – after we'd colonised a few hundred of 'em – clumped together to create the Alliance. Infiltrated by an Order millennia old, it began to impose order and control over anyone it could. They call it a "civilising process" when they want to make the kids feel better about what their parents are doing.
When war broke out between the Alliance, and the Independents, me and mine were more than happy to help out the Browncoats. After all, it was our enemies ordering their executions. But the Alliance had greater numbers, and we got beat. The few remaining Independents were scattered across the galaxy, and we were forced back into the shadows. The longer we rested, the stronger the hold of the Alliance. It seemed, after centuries of fighting, that the Templars had finally won.
Then when all seemed said and done, we got a second chance. Armed with the knowledge that the Alliance created the Reavers, the people started to rise up. The Templar's may still be powerful, but their hold is slipping and they're starting to get worried.
Finally, we have our chance.