When Bubble Puppy disappears after biting an ancient magical bone, it resulted in sending the guppies in a world search for Bubble Puppy.
Fearless explorers Gil and Molly are travelling through the deserts of Egypt with their faithful dog Bubble Puppy. They find an ancient tomb, half buried in the sand, and explore the chamber deep inside. The chamber seems to finish at a dead end, but Bubble Puppy finds a hidden button on a dog statue which reveals a secret passage. They go deeper into the chamber and warn Bubble Puppy not to touch anything. To his delight, Bubble Puppy finds a squeaky bone and can't help but pick it up. The ancient bone emits a bright green light and Bubble Puppy vanishes into thin air!
Molly and Gil go to Professor Nonny for help, taking the bone with them. Nonny identifies the artefact as 'The Bone of Machu Pecchu', a magical bone which teleports any dog that touches it to The Temple of the Lost Puppy. Nonny notices three different shaped spaces in the bone where jewels should be and, when these jewels are returned, the way to the temple will be revealed. Nonny already has the first jewel- a ruby- and places it into the bone, revealing an image of a temple in Japan. With no time to waste, they rush out to find Bubble Puppy.
Molly, Gil and Nonny board a plane to fly to Japan and meet their pilot, Deema.
Her company, 'Whoopsy Daisy Airlines', is named after the many mistakes and accidental nosedives which happen due to Deema's lack of attention, afterwards exclaiming: "Whoopsy Daisy!". On their way to Japan, the guppies sing Puppy Here We Come to help keep their determination and spirits up.
The guppies eventually reach their destination and meet Goby, an archaeologist who knows the temple better than anyone. Goby leads them into the temple as they search for the next jewel- an emerald. They discover a chamber with a big mural on the wall, where Gil finds several shaped buttons. Since the emerald they are looking for is square, they press the square-shaped button, which rotates the wall and reveals the emerald. As they take the jewel, Deema carelessly knocks over a stone statue, breaking a column and creating a domino effect which destroys the entire temple! The guppies manage to make it out in time with the treasure in hand. After placing the emerald into its slot, Nonny discovers their next destination - The Himalayas.
The guppies make it to the Himalayas, but Deema is forced to make a crash landing after narrowly avoiding a huge mountain. They spot a cave and decide to venture inside, finding some very large footprints which they think might belong to a yeti.
An unknown figure casts a big shadow on the cave wall, scaring everyone deep into the cave. As the figure gets closer, however, it turns out to be Oona, who was looking for the Yeti. She leads them further into the cave where there are many jewels and sparkling stones. After finding the last jewel, a triangle shaped sapphire, Nonny places it into the bone and discovers their final location- an island in the middle of the ocean. Just then, the Yeti, which turns out to be real, appears behind them, scaring them out of the cave. They make it into the plane, but Deema can't get the engine running. The Yeti catches them up, but turns out to be friendly and gives them a push, waving goodbye as they fly away.
The guppies find the island; a landmass with a huge active volcano at its centre. They start to explore, eventually finding a big door with two dog statues at either side of it. Each statue has a place for a bone in its mouth, along with a pattern of jewels. After matching the correct pattern on the bone, Gil places the artefact into its slot, opening the large doors.
The Temple of the Lost Puppy is a large outdoor sanctuary where many lost puppies play. The guppies find lots of lost puppies, but Bubble Puppy is nowhere to be seen. Just as Gil starts to lose hope, Mr. Grouper, the guardian of the lost puppies, appears with Bubble Puppy in his arms. Gil and his puppy are reunited, and the rest of the guppies decide to return all of the lost puppies. As they celebrate, the volcano rumbles and begins to erupt hot lava! Everyone rushes to Deema's plane and they take off into the sky, leaving the island behind.
As they sing a reprise of Puppy Here We Come, all of the guppies send the lost puppies down to their owners and fly off into the sunset, ending their adventure.