The kids are on a school trip in Maryland taking pictures of flowers and butterflies. Tom took a picture of a monarch butterfly and it lands on his nose. He sneezes and the butterfly flies off, while Sugar-Belle laughed and then the teacher announced the students that it was lunch time. Meanwhile, Tim was still taking pictures when a blue morpho butterfly landed on his cap. He looked up and said hello to it. The butterfly greets back and tells him that his name is Buddy. Tim decides to take Buddy with him and introduce him to his friends.
While the kids were eating lunch, Tom started to wonder where his cousin was. Tim came with Buddy, still on his cap. The kids approached to him and asked how he found a blue morpho butterfly. Tim explains that Buddy found him, and the teacher announces that it's time to go back to school. Feeling a little disappointed, Tim pointed his finger out for Buddy to stand on and laid his finger on a leaf for his new butterfly friend, then said goodbye to him before he and his friends leave.
Later that night, while Buddy and his friends were sleeping, they hear a vacuum-like noise coming from the other side of the meadow. There appeared a humongous automobile with a giant vacuum hose and riding on it was a mad, mad, mad man who was collecting all the butterflies and destroying their home. Buddy and his sister, Bonnie, managed to escape just in time before the vacuum man caught them.
The next morning on the weekend, Tim was still in bed sleeping when Buddy and Bonnie fluttered into his room and woke him up by landing on his nose. As Tim was finally awake, he was surprised that Buddy and his siser Bonnie was in his room explaining to him that a mad, mad, mad man has killed all the flowers in their home and kidnapped their friends and family. Shocked, Tim with Buddy and Bonnie dashing behind him quickly ran downstairs to call his friends for help before his parents woke up.
As soon as Tim was done with breakfast, he grabbed his backpack with Buddy and Bonnie inside, hopped on his scooter, and rushed to the treehouse in the playground that was near the lake to meet up with his friends. Tyke asks Tim, who was still catching his breath, what was going on and as Tim finally caught his breath, he explained that a mad, mad, mad man has caught all the butterflies and destroyed their home. White Tabby asks why he would take the butterflies, but Tim doesn't know why nor does Buddy or Bonnie. Jerry suggests that they should hop on their bikes, scooters, and skateboards to Maryland's meadow and first clean up the mess in the meadow that the man's machine has made before they could find the butterflies.
They bring garbage bags and gloves to keep their paws safe from any thorns and splinters. As Mary Lou was about to pick up a brown leaf that was runned over,she saw some tracks on the ruined flowers that lead to a dark lair with a black cloud hanging over it not far from the meadow. The gang finally finishes the cleaning and hops onto their wheels to go to the lair.
As the gang finally made it, they approach to a high wooden door. Tom and Jerry used all their might to push it open, and they enter. Once inside, Tim tells Buddy and Bonnie to hide under his cap and the kids put on their invisibility cloaks so the mad man or his henchmen don't see and catch them. They quietly walked through the hallways with creepy paintings and ugly statues, when they hear a menacing laugh going on behind a door with dim light shining behind it.
Quietly opening the door a bit, they saw a giant jar full of blue morpho butterflies trapped and thirsty for nectar. Right next to them was the smirking mad man that captured them. He explains his plan about using the morpho butterflies' wings for his new invention; Blue Morpho Sneaks! Sneakers that don't wear off and will keep the wearer running, jumping, walking, hiking, and even flying! Once the morphos die, he will rip off their wings to make his sneakers and sell them for money.
Tim was furious about the mad man turning the butterflies into sneakers and he was so mad, that he accidentally opened the door wide and the hood on his cloak came off, making him visible. The man spots him and orders his men to get him and his friends. They tried to escape and ran to the door, but the henchmen caught them before they could get outside.
As they were thrown in prison, Tim scowled at the mad man and told him that he will never get away with this. But the mad man was already ignoring his yelling and went back to his lab to get back to work while one of his henchmen stayed behind to watch the prisoners. Feeling despaired and hopeless, Sugar-Belle sat on a bench and said that they will never get out to save the butterflies in time. Tim tells his friends that they shouldn't give up, but Tom asks him "What can we do?" in a sarcastic way. Just then, Tim felt something wiggle under his cap and to everyone's surprise, it was Buddy and Bonnie! Tim then remembered that they hid under his cap the whole time just to stay out of sight. Tim comes up with an idea that will get him and his friends free.
Bonnie distracts the guard by tickling him while Buddy gets the key. While the guard was too busy laughing to notice Buddy getting the key, Buddy quickly turned the key with all his butterfly might and set his new friends free! Then when the guard finally calmed down, he saw that the bars on the jail had been opened up and the prisoners have vanished.
Back in the lab, the mad man was about to perish the butterflies when Tom used his slingshot to shoot a rock at the mad man and it strikes him on the hand. He summons his henchman and they charge toward them. But before they could catch them again, Mary Lou and White Tabby used their perfume to make a thick fog of strong Rosey scent that made the mad man and his men cough. Tim came down from a rope that Tyke tied to a nearby pole on top of a stipple. Then as he got near the jar,he unscrewed the lid and all the butterflies woke up, but they were too thirsty to fly off. Luckily, Sugar-Belle gave Tim a bouquet of flowers for them to boost up their energy. Once the butterflies saw the bouquet, they sipped the nectar out of them and were finally becoming strong enough to fly away. The mad man sees Tim in the jar giving the butterflies the flowers and rushes to his controls to close the giant jar shut just to trap the butterflies again, along with Tim.
But before he got there, Jerry jumped on to him just to give Tim and the butterflies some time to escape. Just as the bouquet was sucked dry, the butterflies flew free and Tim climbed up in time. Mary Lou and White Tabby used every last spray of their perfume to make the fog even thicker and soon, she, Mary Lou, Tom, and Jerry climbed up on the rope just in time before the whole lair exploded.
After their escape, the butterflies flew back to the meadow and Buddy and Bonnie hugged their parents happily, just to finally see that they're alright. Just as the gang was about to hit the road,the butterflies give them some thank you gifts: a magical sapphire that grants wishes and a flight back home.