There are two different ways out of the plant. One involves fixing a lot of stuff. Another involves finding a way to exit the plant without fixing all the faults. Just keep exploring and opening doors.

This is late, but you can still fix the plant if you flushed the keycard.
Hint 1: You need to find a way to access the basement. There's a door on the bottom-most floor, level with the four flocculation pools
Hint 2: All but one of the orange keycard doors can be opened without a card. Check the sign above them. Reactivate the fire alarm: the doors marked as fire exits
Hint 3: You can find an orange keycard for the remaining door (not vital but a handy shortcut) in the basement, in the room with the four big cylindrical tanks, near the stairs to the office.

Flushing the yellow keycard locks you out of a couple of documents about the conspiracy, a funny email, and some batteries. The plant itself can be fixed without it.

(Fixing this plant was much more challenging than the first one, but as a hint: you want to complete a circuit in the right order, so raw water > flocculation > etc. Don't try to fix everything, only redirect the water to the parts that actually work.)

Final hint because I was extremely stuck on this myself: once you've fixed the plant and got vocal confirmation from Mark, you still need to start up the system by pressing the big "start pump" button in the basement, in the room labelled "Sewer Pipes 01 And 02"

I did the same last year and also thought I was stuck. Turns out I had missed some steps in the plant itself to get out of there. It's a large area!

Whew, I almost uninstalled after I realized that I had actually flushed a key card. The dumb train was the exit, not the stairs by the tank labeled exit.