TMP - "Not Again"

So, in the Season 1 Finale of The Magnus Protocol, there is a moment thta I'm curious about whether anyone's mentioned it yet.

The moment is when Alice finaly makes it to the Hilltop center and finds the old "part of the crew, part of the ship" man, she whispers to herself, "Not again".

Do you guys think she's been here before and see this happen?