To find the invisible Captain, wander around near the Chalkboards or within 2 tables of them until you get the "press 'x' to talk to the Captain". This happened to me during the Closed Beta test period.
I'm wondering if this is a loading issue, did you happen to notice if you could still interact with the Captain by clicking X where he should be located?
I went in a third time, and it worked. Also, there wasn't an interact with the Captain in his spot on the map. The ex-resistance guy(?) was invisible (I'm in CR now so I don't really remember much of the details.