The show opens with Shaggy and Scooby-Doo daydreaming about an all-you-can-eat restaurant. Shaggy wakes up realizing that the "taco" he is eating is really Scoob's foot. At the sound of the "breakfast alarm" Shagster decides it's time to eat. They frantically run around the house in search of food but none is found. "Well, at least we still have each other" Shag says.
While at their all time low, Shaggy and Scooby get a phone call telling Shaggy that his Uncle Albert left him and Scooby 1 billion dollars and a mansion. Shag calls up the mystery gang and tells them to make a list of everything they've ever wanted and he would get it for them. So now it's off to their new mansion.
On the way up the steps, Shaggy tells Scooby-Doo how crazy it is that Uncle Albert left him money because Uncle Albert didn't even pass away, he just disappeared. They are greeted at the door by Mr. Shaggleford's first invention Robi, the robot that never had all of the "kinks" worked out. While Robi whips Shaggy and Scooby-Doo up something to eat, they head for the big-screen t.v.
After trying various remotes to try and turn on the t.v., Robi comes in with food. Since the plate got mixed in with the beans, they decide to put aside food for a minute and continue looking for the right remote.
The remote they do find really opens a passageway to Uncle Albert's secret lab. They see tons of inventions such as the teleportation device and the shinking ray. Fooling around with the shrinking ray actually helps the Shagster find a letter from Uncle Albert. The letter says "Use this computer password to access my files". Using the 'Scooby Snack' password, they learn that Shaggy's uncle recently discovered a top secret invention- a formula for nanotechnology.
The nanotechnology lets you transform yourself into amazing things. Even though it is still in the development stage, which means it can only be used on animals, there are still bad men trying to steal the formula. It turns out that Uncle Albert wants them to use their mystery solving skills to find the formula and keep it away from the bad guys. In fear that his life is in extreme danger, Albert tells Shaggy & Scooby that no one will be safe unless they're the ones to find it first.
They then raid the lab fridge and find all the ingredients needed for hot dog tacos, plus a recipe for Scooby-Snacks. They print out the hot dog taco recipe just as Shag tells Scoob what a great guy his uncle is. He can't imagine why anyone would want to hurt Albert.
We then head to a submarine where we find the evil Dr. Phibes and his minions. It seems that he and his field agents are also looking for Dr. Albert Shaggleford's formula. When field agents 3-13 fail to come up with the formula, Dr. Phibes is glad to hear that agents 1 and 2 have video surveillance of his mansion. (It's the same mansion that Shaggy & Scooby-Doo are in.)
Next, we see Agents 1 and Striking Cobra(Agent 2's preferred name) receiving orders to shoot first and ask questions later when infiltrating the mansion. As usual, Shaggy & Scoob are cooking in the kitchen. With the all-important food question settled, Shagster and Scooby-Doo spend time trying to figure out the mystery. Where's Uncle Albert? Where's the formula? Why make Scooby Snack the password?
As agents 1 and 2 storm the mansion, Robi does his best to defend the gang but it didn't stop the lasers from burning the freshly baked Scooby Snacks. The agents chase Shaggy and Scooby-Doo out of the kitchen and into the room Robi is mopping in. Shag and Scooby-Doo won't give up the formula(because they don't know it) and fall into the secret lab(with 1 and 2 squeezing their way in as well). Shaggy has a brilliant idea to shrink Scoob and him so that they won't get caught. This only works for so long as Scooby-Doo accidently steps on the enlarge button. After back and forth enlarging and shrinking, S & S are finally caught in nets.
Our heroes are taken to the submarine where Dr. Phibes tells them that if they give up the formula then he will be reasonable and let them live. Shaggy convinces Scoob that they have the formula and they give it to Dr. Phibes. He then throws them into a chamber and tells them that it will fill with water in 1 minute. Shagster thinks that it is the perfect time for a Scooby Snack but when they bite it they discover that it is covered in metal.
Eventually, Shaggy realizes that everything is connected because his uncle made the nanotechnology formula so that only Scooby-Doo could eat it. He then takes it and it turns him invisible. Shag convinces the agents that Scooby has escaped so that they'd open the door. They do and that is when they burst out of the room and make their escape. Making their way to the main hull, they trick the guards into beliveing that Scooby is a ghost and they all run away terrified. However, once Scooby burps, the power is gone and the only guard remaining fires but misses and hits himself.
The "team" escapes the submarine and leaves Dr. Phibes thinking he has the formula. Dr. Phibes' "formula" however is actually just a recipe for hot dog tacos.
In the end Shaggy and Scooby-Doo learn 2 things from Uncle Albert's computer files. One: according to the recipe, the Scooby Snacks can turn Scooby-Doo into anything and Two: the ability only lasts until Scooby digests the snack. The duo decide to work on their own for a littel until they can find Uncle Albert.
The episode ends with the classic: SCOOBY-DOOBY-DOO!