When you finally regain control, try to move left and right using the left analog stick to knock the chair over. When the guard tries to attack you, counter his attack. This begins a rather long mini-tutorial on countering. Just follow the guards orders and eventually you will be attacked by inmates. Counter these attacks as best you can. You can also attack them yourselves at this point.
This part is more like a regular fight. Despite still being in chains, you can still attack and counter and eventually you'll be freed. Defeat the remaining enemies with attacks and counter attacks. Then when you say something about finding Alfred, head over to the dumpster and the climb up the ladder. At the top, run forward and jump across (just hold A) to the air ducts. Follow the ducts around and jump up by the broken ladder and then climb the ladder at the top up to the roof.
Keep hopping up one ledge at a time until you call Alfred. Once your talk is over, turn right and you should see a tall building with ACE in big letters going down along the side. Line up to jump across and grab the exposed ledge. Grab it and circle around to the side of the building. You'll continue circling around the building in a sort of navigation tutorial. Follow the button prompts and you'll eventually make your way to a ladder and the top.