His team wasn't safe like he expected. Instead, his team was also in danger even though they started retreating.
Atlas didn't know about it, but the Prince had already sent another fleet to this place that had already circled an even bigger area not long after Atlas was caught.
It was like there was a fleet in the center, and then there was another fleet, creating a border in some distance. And in between those two fleets was Atlas' group.
It wasn't that the Prince wasn't going to chase after Atlas' fleet. It was just that he wasn't going to let Atlas do it. He was going to do it once his team was caught. It was only then that he was going to get Atlas to kill them personally.
Atlas entered the ship, having no idea what was happening outside. Instead, he was more concerned about his family at the moment. Lilith was going to locate his sister, but if she couldn't, he wanted to have a backup as well.
As for what kind of backup, he wasn't sure.