The first half of the movie and takes place when the Digi-Destined were real little. It's the re-telling of the story of how the original 8 digidestined became the digidestined. It's the story that was told in episode 45 (The Ultimate Clash). One night, when they all lived at Heighton View Terrace, a Digi-egg appeared on the screen then pops out of the screen and soon the egg hatches to Botamon and then digivolve's to Koromon then to a giant Agumon and then he digivolved to Greymon. They saw the fight between Greymon and Parrotmon. They 8 children who saw the battle grew up to be the digidestined. During the battle a light processed their information leading too the creation of the tags, crests, and digivices. This is also when these devices were linked to the Digimon and children.

Six months after the first adventure in the digital world, it's spring vacation and all the children are scattered around. Joe is writing exams, Mimi is on vacation in Hawaii, Kari is going to a birthday party and Matt and T.K. are in a small town in the country visiting their grandmother. The only people who aren't completely busy are Sora, Izzy, and Tai.

While Izzy is working on his computer, a Digi-egg appears on his screen. Before his eyes, it digivolve's into a small "jellyfish/contact lenses" looking Digimon. Izzy figures that this must be an evil Digimon and gets a hold of Tai. At Tai's house, Izzy brings the evil Digimon up on the screen of Tai's computer. As they watch, the evil Digimon digivolve's again. Tai tries to get a hold of the other digidestined but can't. Sora tells her mom to tell the boys that she isn't home because she's mad at Tai because of an argument over an hair clip.

It seems that nothing can stop this Digimon, but out of the blue, Izzy receives e-mail from Gennai. Gennai wants to send Agumon and Tentomon into the computer system to fight the evil Digimon, but the Digimon digivolve's again into a more powerful being. Izzy receives e-mail from children online all over the world that have been watching the battle on their computers. Certain kids send encouragement while others do the opposite. Meanwhile, the evil Digimon is going from computer system to computer system causing chaos by eating data. Eventually, Tai gets a hold of T.K. and Matt, but they can't find a computer in the small town their in. When they finally find a computer at the local barbershop, Gennai sends them Gabumon and Patamon to aid in the fight. Agumon and Gabumon warp digivolve into WarGreymon and MetalGarurumon, but are still no match for the evil Digimon. The evil Digimon starts a countdown and launches two of the US's missile. Izzy later finds out, the missiles will land in Colorado & in their home town.

It seems all hope is lost but all of a sudden, Matt and Tai get sucked into the computer and help their Digimon. WarGreymon and MetalGarurumon merge into one powerful Digimon, Omnimon, but they still can't stop the evil Digimon. Izzy has an idea and sends e-mail from the children watching to the evil Digimon. This slows him down and the Omnimon destroys the evil Digimon. With only one-second left on the clock, the world is saved from disaster and the digidestined have to say goodbye to their Digimon once again.

One of the kids helping the Digidestined during the battle on the 'Net is an American boy named Willis. At the same time that the first Digimon hatched on Tai's home computer, another egg is hatched in America making Willis the human companion of twin Digimon Chocomon and Gummymon. Soon they digivolved to Terriermon and Lopmon when they got older. One day, Willis was playing with them in a field, and suddenly Lopmon was warped into an evil force field, totally taken over by a computer virus, caused by the electronic battle over the net, thus making him one of the bad guys. He continued to disobey Willis after every command was given. His evil strength made his grow up to be Wendigomon and stalk Willis's every move. There was more trouble brewing when Wendigomon suddenly told Willis and Terriermon to "Go back..." Willis thought he meant got back to Colorado so they head back there.

T.K. and Kari are visiting New York City when Willis' lost Digimon, Kokomon, appears. T.K. and Kari follow Willis and Terriermon (Willis' good Digimon) across country while Davis, Yolei and Cody get an e-mail from Kari that tells them to join them.

When the team finally comes together, the battle begins. It wasn't till then that they realized what Wendigomon meant, he meant to go back to the beginning. Willis is unable to get through to his Digimon and the renegade Digimon is unwilling to listen to his twin brother, Terriermon. It seems all is lost until Gatomon and Patamon Digivolve to their Mega forms, releasing the golden Digi-eggs. This Digi-eggs allow Veemon and Terriermon digivolve to Magnamon and Rapidmon. The destroy the virus and set Kokomon free.