At Paul's Pizzeria, Punk Rock is jamming to the jukebox, while the Giggler is snoozing next to him. In a nearby booth, Rex Ruthless, Bratman, Dirty Trixie, Misty Magic and Weatherman are enjoying their pizza. Weatherman asks Misty Magic to pass the salt and pepper, but when she uses her magic to serve him some, she can't seem to turn it off, and the pizza is buried in salt and pepper, which causes Weatherman to sneeze, and his weather manipulation powers generates wind from his sneeze, causing the pizza to blow across the booth right into Rex Ruthless' face. He is hurled backward to the booth behind him where Captain California and Glorious Gal are seated. When Rex starts to speak, Captain California tells him not to talk with his mouth full. Just then, the Human Fly flies over and lands on Rex Ruthless's nose, he believes it to be a fly and tells him to shew. Bratman jumps up on the table with a rolled up newspaper and tells him he'll swat it, but he slips on the pizza and Captain California grabs the paper and Bratman falls into the jukebox with the pizza falling on his head and spinning like a record. This caused the music to stop, and just then Punk Rock asks who turned off the sounds. The Giggler, now awake, laughed. Captain California unfolds the newspaper and tells Glorious Gal to direct her attention to the headline, which talked about how the Human Fly stole a gem. He stole a million dollars in jewels. Across the room, Punk Rock fixes the jukebox, and gives it a kick. But just then they realize that since the wires had gotten crossed, they somehow managed to tune into the police broadcast, and they can hear Chief Hardy's voice. He says they're going to set a trap for the Human Fly at the museum. The heroes decide that that would be fun. Unfortunately, the Human Fly who is on Captain California's shoulder, hears everything.
Later, at the museum, the heroes and Chief Parker check out the Tiger's Eye emerald. The heroes marvel at the emerald's beauty. Misty thanks her uncle for letting them check out the place. And he said it was a good excuse to keep an eye on them. Giggler checks out the emerald and the Chief grabs him by the collar. The Chief's officers then engage the security system, and Peter Penguin accidentally sets off the alarm with his beak. His armed police force run over to a the penguin instantly, who had been encased in a cell by the security system. The Chief says "Not bad." Captain California tells the Chief that with such a set up, there's no way the Human Fly could get away with the Tiger's Eye. And the Chief tells him even if he does, he won't get the real Tiger's Eye, but a fake, because he put a fake in the display and the real one in his pocket. But unbeknown to to everyone, the Human Fly was clandestinely observing the entire situation. Not long later, the exhibition is full of customers. Captain California suspects that the Human Fly could be among all of the people. They see a guy in a hat and scarf and suspect that he could be the Human Fly in disguise, and so Misty Magic uses her magic to remove his disguise, and she sees that it's actually an undercover cop. Rex Ruthless decides to use one of his gadgets that makes him fly to take a bird's eye view, but in the process he collides with Weatherman, who was already doing the same above. The two of them fall on top of one of the ceiling rafters. Angered, Weatherman begins to attack Rex with his weather powers by blasting lightning out of his hands at him. But in the process he accidentally creates a rain cloud that causes it to rain inside the museum. The Chief is angry. And Bratman steals an umbrella from A.W.O.L....just then, the Chief tells the young heroes in training he wants them out of there now. Elsewhere in the museum, the Human Fly is watching the commotion. Just then, a man storms through the door and the Chief is hit by the door, and he falls to the ground in a daze. The man says his name is Professor Bumpkin, and he has come to see the emerald, but upon looking at it he realizes that it's a fake, and he complains, saying that he will sue the museum for such falsehood. The Chief asks him politely to calm down, but he continues to cause an uproar. The professor then grabs the emerald and says it's a fake, just then the security system kicks in and the Chief and the Professor are encased in the security cage. Peter is then chasing the Human Fly, but the others don't know it's him, but they follow, but he hides in a circuit box, and then cuts a wire and the power goes out. People start to panic in the dark, and the Human Fly takes the opportunity to get into the Chief's pocket and steal the real emerald. The young superheroes chase after him, and once power is restored in the museum, and the chief is freed along with the professor, the professor asks "What is the meaning of this fake?" The Chief tells him that it was just bait to trap the Human Fly, and that he has the real Tiger's Eye on his person...but when checking his pockets he realizes that it's gone.
Meanwhile, outside, the superheroes continue their pursuit of the Human Fly, who is carrying the Tiger's Eye, flying through the sky. Weather man uses lightning attacks, but the Human Fly uses his super strength to punch the lightning, and it goes flying after Peter Penguin, who was hiding in a cloud, and he ducks for cover in a Flower shop. But he doesn't fare so well when the lightning strikes the flower shop and he is shocked. Meanwhile above, the Human Fly knocks Weatherman, Giggler and Bratman off of his rain cloud, but Captain California, Glorious Gal and Misty Magic catch them. But when Misty catches Weatherman, he is to heavy, and the two of them drop and she gets help from AWOL. And they crash to the ground. The Human Fly continues to escape, heading toward the City Dump. They are worried that they will lose him in there. He begins singing the Lone Ranger theme song except with the lyrics "To the dump, to the dump, to the dump, dump dump!" The Human Fly continues toward the dump and Rex flies toward him but accidentally crashes into a billboard sign that advertises the City Zoo. Peter Penguin then takes a Venus fly trap from the Flower shop and returns to pursuit after the supervillain. The heroes are convinced that this might work. They head him off at the pass, and at the dump, Misty uses her magic on the plant to make it grow, but instead it turns into a crow. They then create a fly paper net and Punk Rock sees that the Human Fly is approaching with his Binoculars. Misty continues to try and use her magic to make the venus fly trap grow, but unsuccessfully. The Human Fly continues to approach, and he still is singing the Lone Ranger dump song. First they try the fly paper net, but he rips right through it. Misty continues to try to make the venus fly trap grow. She is finally successful and the venus fly trap grows and swallows the Human Fly.
Later, back at the museum, the Professor is happy that the real emerald is safe again. And he thanks the Chief. But the Chief humbly admits that the credit goes to his niece and her friends. She then thanks him. The Chief holds up the small caged villain and tells him that they're clipping his wings. Glorious Gal then asks the Professor if he can really tell the two emeralds apart. And he points to one and says that this one's the real Tiger's Eye. But Chief Hardy tells him that the other one is the real one. Punk Rock says; "Reality!" And is inspired to play a song on his guitar. The musical vibrations of his guitar caused the fake emerald made of glass to shatter. The Chief then has the Professor hand over the real emerald.