I don't think it shocks anyone that Michael is alive after being shot at the end of "Guilty As Charged." "Eyes Open" takes place a mere three days later, as all of John Barrett's misdeeds are being exposed, and he's recovering from his injuries in the hospital. There's a great callback to the Burn Notice pilot when Fiona kicks him in an attempt to get him to come around, just as she did to wake him up when he was first dumped in Miami.
Once Michael is up and moving, he wants to pick up where he left off, much to Madeline's annoyance. The hospital is the last place he'd like to be.