Maintenance for the week of April 7:
• PC/Mac: NA and EU megaservers for patch maintenance – April 7, 4:00AM EDT (8:00 UTC) - 9:00AM EDT (13:00 UTC)
• ESO Store and Account System for maintenance – April 7, 9:00AM EDT (13:00 UTC) - 6:00PM EDT (22:00 UTC)
• ESO Store for maintenance – April 10, 12:00PM EDT (16:00 UTC) - 3:00PM EDT (19:00 UTC)
it seems like the captain is stuck in the doorway near the bow of the ship. I went in that room and logged back out then in, and when I went through the doorway, the captain spawned. It seems like if she is stuck like that, you will have to fight her there.
I first noticed this location when I keep logging in and out, and when I pass the other doorway. for some reason I was able to see the captain, but as soon as I leave the doorway she disappears,
Guys - to fix this in the meantime, please log out (or use /camp) in the doorway where the Mob is meant to spawn. If you kill her as you log in, you can progress.