Let's check couple of things. Have you entered the train?
Yes, I got into the train and the other side
Good, did you notice there's a platform on the darkside, as well. You just need to get past Chief Ghouley.
I have access to the darkside platform
Then you should visit the darkside control room. The key is hanging on the key rack.
Agent McScream won't let me through with the key
Oh, he spots the key. It's evidence. You have to find another way to smuggle the key through. You can put the key back into the control room rack while you try to find a way.
You didn't get rid of it. You just moved it to the darkside toilet.
What to do with the tentacle?
Give the control room key to the tentacle. Then use the plunger again into it and it will appear, with the key, on the brightside toilet. You can now use the key to open the control room door.