gravetitan

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!