The Alliance is the AngloSino Government. They are in charge of pretty much everything in the ‘Verse. If the crew of the Serenity are the heroes of the show, then The Alliance are their nemesis, chasing them down for their criminal activities and to recapture a certain passenger on board. I’m sure they believe they’re the good guys, but considering the dodgy things they get up to in secret, and, of course, that they are permanently on the case of our crew, we have to hate them.
There’s just no getting around it.
Down with the Alliance!