Bobby was expecting to get vaporized right then. If the Badoon didn't do it, then the laser cannons would.

When someone fell from the sky to attack the Badoon, he wasn't sure what to think. He looked up and saw what was, quite possibly, the third-coolest ship he'd ever seen in the area.

Then there was a flying Skrull! He didn't even know that Earth /had/ Skrulls!

The Badoon saw that the tables were turning against them. Those that could flee, fled back to their ship. They wanted to get airborne before Earth's defenders came at them. It would be hard to explain their failure, but getting captured would be far, far worse.