i was wandering around Monarch for a bit and headed back to the ship to swap out a companion for SAM, but when i got there he had vanished. nowhere to be found on the ship and when i go to leave the ship he's no longer available to select as a companion. is this a glitch? is this part of the story? i saw another post on reddit about the exact same thing happening to someone else but i havent seen it mentioned anywhere else!

Could be related to Parvati disappearing... don't know if there have been any solutions, but you should check the corresponding threads. Supposedly, team member can "die" when they are on a ladder at the moment you leave the ship or something.