Riding pretty rough, seems like theres resistance or hesitation in acceleration.

My car has been slightly hesitating upon acceleration, sometimes it will get to 3000 rpm's before it even hits 25 mph. Tonight it started chugging really bad, as if I was low on fluids and the check engine light came on and beeped and flashed. I chugged into a gas station and checked my fluids, they are fine. Put gas in. Still did it. I do need my rear brakes done badly, but that could not be the problem, could it?