To open the vents, a terminal in the Facilities mainframe needs to be accessed. To get there, successfully complete Escort Technician in Facilities One and Connect Circuits which opens the door the Facilities Three. Then fire up the power there (southeast room) and backtrack/puzzle your way through red and green beams. The red laser beams have to be switched off with a nearby console (5000 damage and death otherwise!); the green beams can be jumped over. Or hit them and deal with a laser robots. Pick up the Shop-Tec parts for the Shop-Tec at the entrance for some extra experience.
At the last section of Facilities Three in the northeast area, crawl under a disfunctional lasergate that has the lowest beam missing and take out the turrets a little further up ahead. Then after the cutscene showing nightkin cloaking themselves, enter the mainframe room, kill all the nightkin and use the terminal to disable the vents. Return to Patty in the Gardens through the exit door.