The all-crew completion goal
All Aboard! requires you to finish the game with all stranded Neera aboard the Expedition Spacecraft. If you want an all-crew finish, make the rescue condition your checklist before completing the game.
Mission Complete! is the separate achievement for finishing the game. Completing the main story and completing the all-crew rescue goal are different requirements.
Start rescuing crew early
The early route involves Atiel and Nim Idal. Help Atiel reach the spacecraft, restore the Surface Elevator, then speak with Nim Idal so he heads to the ship. The early walkthrough places these events in order.
The achievement condition is about the crew aboard the ship at completion. Do not substitute collecting a single orb for that crew requirement.