Basically, this is the ability for heroes or villains to switch sides and maintain their archetype (character class). So a brute could become a hero, or a scrapper could become a villain, for instance.
The Going Rogue system is a new game dynamic for City of Heroes and City of Villains that allows players to alter the morality of their characters, eventually opening up the opportunity to turn their Hero into a Villain or vice versa.
This could help undo one of the worst decisions the City of Heroes developers ever made: splintering their player base. With two separated worlds for people to play in (hero side or villain side), they effectively made both sides emptier. Over time, people gravitated mostly back to the hero side, leaving villain side almost completely empty. My guess is that this going rogue system will eventually finish off the "villain side" of the game as anyone who wants to play a villain character class will simply go rogue right away and then team up with their friends "hero side."