How to Get Gordon Out of the Medical Facility in "Batman: Arkham Asylum"by Dan Ketchum ; Updated September 22, 2017
During his journey through the eponymous nuthouse in Batman: Arkham Asylum, the Dark Knight busts a lot of heads. From taking down iconic villains to flooring dozens upon dozens of the Joker's goons, Batman doesn't seem to do much in the “saving lives” department until he rescues his longtime ally, Commissioner Jim Gordon, from the clutches of Harley Quinn and the Joker in Arkham's Medical Facility. While you'll spend plenty of the game on Gordon's tail, your mission to finally free him starts as you exit the Medical Facility's morgue after your encounter with Scarecrow.
Head through the morgue door's into the lower corridor area of the Medical Facility. Follow the green arrows until Batman comes across the dead body of an Arkham guard, causing him to realize that he had actually hallucinated Gordon's death due to the Scarecrow's fear gas.
Take down the thugs that burst out of the double doors, then proceed down the corridor, following the arrows to a single closed door. Open it to enter the Experimental Chamber. Move forward to find a pane of glass separating Batman from Gordon, who is guarded by Harley Quinn. After Joker's monologue, the objective “Rescue Gordon without being detected” appears.
Open the vent on the baseboard and head into the ventilation shaft, then drop down and go into the next vent. At the end of the shaft, kick open the vent. Stay in Detective Mode to keep track of the four henchmen in this area -- you'll have to take them all down silently. Sneak up to the first one and use a silent takedown, then break open the vent to the right and crawl in.
Hang a left, a right and another left to exit the ventilation shaft behind your next stationary thug. Use another silent takedown to eliminate him. Stick close to the vents and observe the lower level until the goon there makes his rounds. Crawl behind him with a silent takedown, then head up the ramp and do the same to the next bad guy.
Go all the way up the stairs and grapple above the door. You'll be on top of the cell holding Gordon and Quinn, which, as Detective Mode tells you, is made of fragile glass. Crawl over the glass and when the prompt appears, use a Takedown to break through it and take out Harley. In the ensuing cut scene, Batman frees Gordon from his bounds.
Practice patience as you take down the thugs surrounding Gordon's chamber. If you're spotted, you'll have to start the whole process over again.