Matt, Gabumon, Joe, and Gomamon are being forced to work at Digitamamon's diner to pay off a meal. DemiDevimon sets off a series of accidents that makes Matt question Joe's friendship. Matt overcomes his feelings when Joe is willing to sacrifice himself to save T.K. Matt's Crest glows and Garurumon digivolves into WereGarurumon and defeats Digitamamon.

Tai and Agumon return to the Digital World to find Tokomon. Tokomon relays what has happened in the time that they have been gone (which is several weeks in DigiWorld time). He reveals that the entire group has separated and that DemiDevimon has tricked T.K. into becoming his "friend." T.K. realizes DemiDevimon's trickery after Agumon exposes him for a fraud. Tokomon digivolves into Patamon and drives DemiDevimon away.

Tai and Koromon meet with Kari in Tokyo. They discover that Digimon are appearing in the Real World and decide they must go back to the Digital World to help their friends. After Koromon digivolves into Agumon to battle an Ogremon, a portal opens back to the Digital World.

Tai manages to rescue Sora. Datamon pulls himself, Etemon, and many of Etemon's minions directly into the Dark Network. When Etemon reappears, having fused with the network, Greymon digivolves into MetalGreymon to fight him. The battle ends up opening a portal that sucks away Etemon and transports both Tai and Agumon back to Tokyo.

The discovery of T.K.'s Crest of Hope reveals a cave engraved with Digi-code. Izzy receives an e-mail from Datamon asking for help from within Etemon's headquarters, which is a large upside down pyramid. Datamon promises them that if they free him, he will show them Sora's Crest. After he is freed, however, he escapes and kidnaps Sora. He intends on making a copy of her so that he can control Biyomon.

The group is attacked by a Kuwagamon and Tai fails to digivolve Agumon. Piximon intervenes and saves them. He then offers the group training at his facility, and leads Agumon and Tai into a cave while the others stay outside. When Matt finds his Crest of Friendship and Izzy finds his Crest of Knowledge, they are spotted and attacked by Tyrannomon. Tai and Agumon reappear just in time to defeat Tyrannomon.

After getting lost in the desert, the group is taken aboard a ship helmed by Kokatorimon. Kokatorimon captures all the boys and their partners. Biyomon and Palmon digivolve and defeat him when his ship crashes into a giant cactus. The top of cactus then opens up to reveal Mimi's Crest of Sincerity.

While traveling in the desert, Joe's Tag reacts, leading the group into a Roman-like coliseum. There, they are trapped by Etemon, and Greymon is forced to fight another Greymon. After Joe finds his Crest of Reliability, the group escapes. Tai attempts to force Greymon to digivolve. Greymon digivolves into SkullGreymon and loses control of himself—attacking the others who are unable to stop him. SkullGreymon eventually reverts back to Koromon and apologizes for his behavior.

The kids arrive in a Koromon village overrun with Pagumon, who trick the kids and kidnap Tokomon. Etemon learns of the arrival of the DigiDestined and confronts them. He uses his Dark Network to prevent the Digimon from digivolving and then traps the group inside a cave where they discover their first Crest, Tai's Crest of Courage.

A mysterious person named Gennai appears as a hologram after a fight with Devimon and urges the group to travel to the continent of Server in order to defeat another enemy. Gennai also tells them about objects called Crests that will allow their Digimon to digivolve even further. They build a raft and leave File Island, but are soon swallowed up by Whamon who is still under the control of a Black Gear. After the gear is removed, Whamon takes the kids to where their Tags—the objects that the Crests are stored in—are hidden.

The entire group reunites and is attacked by Leomon. After Leomon is defeated with the light of the Digivices, he tells the children about the prophecies of the "DigiDestined." The group goes back to Infinity Mountain for the final showdown with Devimon. There, Devimon absorbs many Black Gears and grows in size and power—turning the fight in his favor until Patamon digivolves into Angemon and destroys him. Angemon, having used up so much power, reverts into a Digi-egg.

T.K. and Patamon end up in Primary Village, the place where all Digimon are born. There they are confronted by Elecmon, the guardian of the baby Digimon. He struggles with Patamon, having mistaken the two for intruders. To avoid a fight, T.K. proposes that they settle their dispute with a tug-o-war. Patamon wins and earns Elecmon's respect and trust.

After suffering an attack from Ogremon at sea, Joe and Gomamon find themselves on an island with Sora and Biyomon. They are captured by a band of Bakemon intent on eating them. Gomamon and Biyomon manage to escape and digivolve to fight the Lord Bakemon. They eventually defeat him with help from Joe's repetitive chanting.

Mimi and Palmon are harassed by Sukamon and Chuumon. After escaping them, they cross over to the next island, where Izzy and Tentomon landed. After they reunite, Mimi and Tentomon get lost in a labyrinth and are attacked by Centarumon. Izzy and Palmon finally find them and their Digimon battle and destroy Centarumon's Black Gear. After the battle, Leomon appears and attacks the children, but is driven back by the light of their Digivices.

Elementary school teacher Natsuko is struck while working at school and pushed off the stairs in front of the park. Conan and his companions question Sugamoto, another teacher who had planned to walk her home, and parents Ueno and Kandachi, who had appointments to meet with Natsuko. Conan notices something strange while listening to their stories. Later, the police review a photo of the answer sheets Natsuko was grading. Jodie and Camel fail to discover any information that could help them solve the crime from the photo, but Amuro and Conan realize who the culprit is after seeing the picture.

Taki-sensei's proposal relieves the upset within the band, and everyone returns to practicing. Reina no longer isolates herself either, much to Kumiko's relief. But then she sees Yuko, who's been antagonizing Reina, speaking with her.