The ship was something that Lin Fan could control remotely with the automated driving that had been installed. That was how they were able to escape with just the four of them and not a crew to drive the ship.
Lin Fan controlled the ship so that it was in space above where they currently were.
Once the ship was positioned, Lin Fan summoned out a bunch of pets.
There were many injured people, so it was very unlikely that they would be able to move on their own. The only thing that he could do was rely on his pets to carry them into the ship.
But before they could do that, Lin Adam sent out Brainy's puppets to scout out the surrounding area. Working with the soldier who had the earth laws, he created holes that would allow the puppets to reach the surface.
Once they were on the surface, they quickly spread out all over the planet to look for traces of the Beast Race.