Okay, hold-up.

How did they get aboard an O'Neil cylinder station?  They were in the Wide Roaming Lands and down, down, down water features until they hit the outer sea of the Nested isles.

oh, so when Sworn went missing Ioq looked for her and found burnt machinery severed neatly on the unburnt ground?  He activated the portal and went through?  Tixa's a real stand-up guy.

Okay, so, when you say, Mulder, you don't mean--  Oh, you do mean Mulder and Scully, and she's there too, on this O'Neil station?  Why?  Hmm...OK, I guess.