Damn! That is a bug haha I should have disabled the death for the player as there is no UI showing your life.
The ship shows up around midway vertically, in the side opposed to where you are when you get the message telling to go back to ship. It has an icon in the minimap when you get close
If you want to try again, use Ctrl+F1 cheatcode for super-speed so you can speedrun it and see the final cutscene (which is relevant)
(I get the samples and place the scanners in less than one minute doing that =p)