For example, the Empire in Star Wars? They're actually the good guys.
Similar to yours, in The Matrix the computers are the good guys. The humans and the computers share a special synergy, but at first humanity resisted the paradise they were given. To counteract and keep the humans safe, a second matrix was created to mimic real life and protect it's inhabitants, not enslave them. It's also worth pointing out that in the original script people were used as extra computing power, not "batteries".
I like the "R2D2 was a very active primary rebel field agent" theory : http://www.jeepforum.com/forum/f7/reconsidering-star-wars-r2...
You can relax, I'd never want to turn this into.. that. I merely stumbled upon this theory last night and wanted to see if anyone else has thought of or come across some unique or mind-boggling theories.
Haha, to quote an older Hubski veteran in regards to the inflow of people like us, "#askhubski is already turning into Askreddit 2.0". Maybe that's not what you want, but this exact question has been posted COUNTLESS times on Askreddit, and I would know. Ugh shudder
Honestly, I haven't bothered to check AskReddit in a very long time. I wasn't aware. :p Sorry 'bout that.