Is it not obvious ? He took him out into the desert to make a move on Seaweed. But before he had the chance he made the mistake of driving 3 hours towards Rachel Nevada . That is right near as you probably already know where Area 51 is located. This is where the Aliens are.
They most likely levitated them up into the ship. That is more cost effective then beaming them up for the creatures. So that part at least was probably fun and Seaweed would have enjoyed that and the view. But things would get worse for both of them on the ship.
All the Aliens get when they monitor our airwaves BLM rallies and the TV sitcom Chucky and bits of Gilligans Island. On their planet the professor is considered a God and they want to reproduce with Lovey . Not sure why they picked her to be honest maybe her hats.
They would have done implants all over them and will track them hoping to see if they can find some of the Chucky dolls. They believe they need to stop them so they do not end up killing Lovey. Again it has to be her hats.
After they were done they will have missing time and they would have left them at the Little Ale inn and $50 so they can buy a nice breakfast they do have good food i have eaten there . Seaweed probably had enough to even buy a little Alien keychain for a souvenir after he finished his Omelet . It came with Home Fries and toast.