Scooby-Doo and the Alien Invaders (2000) on Netflix

A cosmic case of UFOs, intergalactic intrigue and out-of-this-world romance launches the Mystery Gang into their most unearthly adventure ever. Stranded in Roswell, New Mexico, the gang soon discovers the place crawls with UFO buffs, secretive scientists... and less-than-friendly alien invaders. Then after being chased by aliens and beamed aboard a UFO, Shaggy and Scooby-Doo fall head over heels in love with Crystal and Amber. The gang investigate the mysterious sightings which lead them to a government research base and a huge network of caves hidden under the town.