Scooby-Doo and the Alien Invaders is the third of a series of direct-to-video animated films based upon the Scooby-Doo Saturday morning cartoons. It was released on October 3, 2000, and it was produced, starting in 1999, by Warner Bros. Animation (though it had a Hanna-Barbera Cartoons logo and copyright notice at the end). Unlike the previous films, in spite of the grimmer atmosphere, it also had a lighter tone since the real monsters are the good guys and the disguised humans are the primary antagonists. It is the third of the first four Scooby Doo direct-to-video film to be animated overseas by Japanese animation studio: Mook Animation.
The Mystery Machine is driving through the Mojave desert. A sandstorm comes up and Shaggy makes an wrong turn onto government property. Seeing a UFO causes Shaggy to lose control of the vehicle and the gang find themselves on the outskirts of a small town. While Scooby and Shaggy stay with the van the rest of the gang enters a local diner to get directions. Shaggy and Scooby then see a mythical animal called a jackalope. The run into the diner in panic, claiming to have seen aliens.
The waitress, Dottie, says that they never see aliens but do see strange lights and hear sounds at night. The chef, Sergio, says that a month earlier local cattle vanished without a trace and a lot of people moved away. A man named Lester claims to have been abducted and he believes the two. He also claims to have pictures, so the gang goes to his house to see them. They are nothing more than paintings by Lester, however. He then refers to SALF: the Search for Alien Life Forms (similar to S.E.T.I.), dishes, saying that ever since they were installed there have been numerous UFO sightings and disappearing livestock.
The gang stays overnight at Lester's home with Daphne and Velma sleep in a bunk bed and Fred sleeps on the couch. Scooby and Shaggy fall into a deep sleep on the roof, and are abducted. The aliens try to examine the two, but Scooby is able to free them. After escaping from the ship, they find themselves in the middle of desert, where they again fall asleep. They are awakened by a hippie photographer named Crystal, and her golden retriever, Amber. Scooby and Shaggy fall in love with them. They meet up with the rest of the gang in the cafe and are so love sick that they don't want to eat, which shocks the rest of the gang.
Velma, Fred and Daphne meet the crew of SALF, Steve, Laura and Max, while Shaggy and Scooby hang out with Crystal and Amber. Velma becomes suspicious when she sees dried mud on their boots, since they are in the desert. Later, she takes the gang to a canyon where she believes a seasonal river runs. The canyon proves to be dry, but they find caves, mining equipment and on the cave walls, gold. The SALF crew capture and tie them up. The crew explains that they stumbled on the gold cave while searching for a new location for another SALF dish. Since it was on government land, they decided to keep the secret for themselves, and they planned to keep it that way. They are also exposed as the "aliens" who abducted Scooby and Shaggy, with the UFO being nothing more than a dressed-up helicopter.
Eventually, Crystal and Amber reveal themselves to be the actual aliens from a planet 20 light years away. They dressed like hippies because their only information about Earth came from 1960's television broadcasts. The UFO that ran Shaggy off the road was actually Crystal's. The SALF crew and their accomplices are arrested. Shaggy and Scooby are broken hearted but a box of Scooby Snacks helps them forget about their heartache.
- False MP's
- Scott Innes – Scooby-Doo, Shaggy Rogers
- Frank Welker – Fred Jones
- Mary Kay Bergman – Daphne Blake
- B.J. Ward – Velma Dinkley
- Jeff Bennett – Lester
- Candi Milo – Crystal, Amber
- Mark Hamill – Steve
- Audrey Wasilewski – Laura
- Kevin Michael Richardson – Max
- Jennifer Hale – Dottie
- Neil Ross - Sergio
- When Shaggy and Crystal are viewed from a distance walking together and talking, you can hear him telling her the story about his first encounter with the Witch's Ghost, the previous animated release. This is not the first time continuity was shown, as Scooby-Doo and the Witch's Ghost also continuity from events in Scooby-Doo on Zombie Island.
- Jennifer Love Hewitt performed Scooby Doo, Where Are You? for the film. The track was played when Shaggy and Scooby were being chased by the "fake aliens".
- "Groovy", another main movie track, performed by Scott Innes as Shaggy (and in part, Scooby Doo) saw Shaggy in one of the most rare scenes where he kisses a girl on the lips (Crystal), but it was all just a dream sequence.
- Alien Invaders is notable for Mary Kay Bergman's final performance as Daphne as this film is dedicated to her. It was released almost a year after her death. Grey DeLisle would take over after Bergman's passing.
- One of the bad guys (played by Mark Hamill) almost says the famous "And I would have gotten away with it, if it weren't for you meddling kids!" but before he can say "meddling kids", he is ordered silent by a police officer.
- Crystal and Amber's 1960 outfits were a tribute to the era when the original cartoon series was held.
- This is the second time Mark Hamill (playing Steve) portrayed a character in the direct-to-video series of Scooby Doo. He also played Snakebite Scruggs in Scooby-Doo on Zombie Island.
- During the song that Shaggy sings, he says that when he and Crystal get a house they'd fill it with stuff from 1969, the year that Scooby-Doo, Where Are You! first premiered on television.
- This is the second Scooby Doo movie to be written by comedy writer Ryan T Young (Lampoon/Airheads/Halfbaked)