Happy Birthday, Scooby-Doo is the first episode of The New Scooby-Doo Mysteries.
Driving through the city, the gang, answering as the "Scooby-Doo Detective Agency" gets a call about a robbery at the TV station. Scooby-Doo is only concerned about it being his birthday, which no one seems to remember. Looking for his birthday cake in the oven, he gets covered with Scrappy-Doo's invention--crazy rubber. Daphne Blake and Shaggy Rogers drive him to the TV station, ZPOP.
At the TV station, ZPOP, they look for a "howling ghoul". Scooby is sent into Studio 1 to look for him, and is locked in the dark. Sad, he sings "Happy birthday to me", and is surrounded by dozens of eyes. It is a surprise birthday party on stage! The howling ghoul myth was made up for the surprise, but a real fiend is shown lurking around.
Mark Winkendale presents Scooby a book, Here is Your Life, Scooby-Doo, and Scooby is dressed up like a king. He faints in embarrassment, and the station director, Milo Spender, runs in shouting, "That's not in the script!" Scooby wakes up to birthday cake, but is grabbed away to the show.
The first piece is a film of baby Shaggy and Scooby and their monstrous babysitters. The fiend on the catwalk drops a light, nearly splatting Scooby.
Next, Scooby is asked to remember a couple of voices: "Jinkies!" and "Let's split up!" It is old gang members Velma Dinkley, now an apprentice research scientist for NASA, and Fred Jones, now a mystery writer. Meanwhile, Scrappy and Daphne search and find that the light had been unscrewed.
Freddy and Velma retell one of Scooby's old cases--the Red Skull, who had stolen a diamond necklace from Mrs. Vanderwheel, was captured by Freddy and Scooby, and turned out to be Stuyvesant, her butler. As he is arrested, Stuyvesant angrily vows that he will get even with the gang. Mrs. Vanderwheel now comes out and greets Scooby. By now, Freddy is missing, as is noticed by Daphne. When Scooby boasts of having defeated the Red Skull single-handedly, the Red Skull (the fiend seen earlier, who dropped the light) comes out of the TV screen he was on, shouting, "You haven't defeated me!"
Scooby runs, and is twirled around the microphone, and the Red Skull steals Mrs. Vanderwheel's necklace -- again! Scooby and the Red Skull both get twirled by the mike, and the Red Skull lands on a catwalk while Scooby is left dangling from a rope. The Red Skull wishes him a happy last birthday and unties the rope. Scooby falls and is saved by a piece of crazy rubber that Scrappy finds, stretched out by his friends.
Freddy shows up, and the director asks him, suspiciously, where he was. Everyone splits up and searches, (Scooby being motivated by Velma telling him his birthday present is hidden backstage) while Freddy goes to get the police.
Scrappy and the girls fall through a vent. They find an ascot, which Fred claims as his own. He then remembers he also left his briefcase in the washroom. Scrappy and the girls feel that Fred is acting "too forgetful".
Meanwhile, the camera crews follow Shaggy and Scooby, searching for Scooby's present. Soon, they find the Red Skull. They disguise as French chefs and make "crepe du Scoobettes". Police Chief Bundy arrives as Shaggy and Scooby are running from the Red Skull.
Scrappy goes to catch the bad guy for ruining his Uncle Scooby's birthday, and pulls out Freddy, in whose briefcase are red screws. Scrappy adds up the clues on his wrist computer, which suggests the bad guy is Freddy. The officer tries to arrest him, but Freddy escapes.
Shaggy and Scooby are up on the roof talking about how only someone real stupid would be up there on a night like this in a thunderstorm, and the Red Skull appears regardless. He chases them to a ledge. Scooby rearranges the station billboard to read "RELP!", and the others see it (Fred already in custody), and run to the rescue. Scrappy trips "numb skull", who then winds up dangling below Shaggy and Scooby.
Back on stage, he is unmasked, and turns out to be the TV station director, Milo Spender. He claims it was just a gag to liven up the show, and that he was going to return the diamond. But since he kept trying to pin the crime on Freddy and squish Scooby, the gang knew it was really the revenge of Stuyvesant the original butler on the ones who caught him. They remove a second mask, revealing Stuyvesant. Scooby is praised for capturing the Red Skull twice.
The show ends with everyone singing "Happy birthday Scooby Doo", to the tune of "Frere Jacques".
- The "first babysitter" flashback has a woman with a Bride of Frankenstein hairdo, like the one in the A Pup Named Scooby-Doo episode "The Babysitter from Beyond". Possibly that episode referred back to this one, and it is meant to be the same babysitter, except that the one from "The Babysitter from Beyond" had a normal human skin tone, and this one is inhumanly green and has bolts on both sides of her neck.
- This is Freddy and Velma's first appearance since "The Ransom of Scooby Chief". Fred's and Velma's surnames are revealed to be Jones and Dinkley, respectively.
- Instead of Shaggy going with Scooby-Doo while Fred goes with Velma and Daphne, it's vice versa: Fred goes with Scooby-Doo while Shaggy goes with Daphne and Velma, and in so doing, Fred picks up Shaggy's frightened mannerisms.
- According to Fred, Scooby's greatest mystery is not one the audience has already seen, but one that has occurred off-screen, called the Red Skull Curse Case. This original mystery in the flashback clearly must have occurred some years before Scrappy-Doo joined the gang since he wasn't featured in the flashback, so the Red Skull Mystery must've occurred sometime between 1969 and 1978 (at least in real-world time), though the exact number of years isn't specified.