After you run through the northern sewers and get the job from the board to clean up you may run into a snag at least on ps3. For some reason after you clear the mutants it doesn't tell you the missions done. What happens is you'll start hearing a mutant and you will get hit by projectiles. I wondered why this was happening, i was not getting the mission complete pop up, at first I thought I was screwed because I couldn't finish, I spent a half hour running back and forth trying to find the invisible mutant. Finally I said I'm done and left the sewer, at that point the mission was complete.
So if you get stuck trying to find this mutant just leave and you should see the mission is done. It will not pop up but it'll be complete. Maybe this will save you some time if you run into this problem.