T.K. is attacked in Primary Village by Leomon and Ogremon, until Tai, Matt, Izzy, Mimi, and their Digimon arrive to his rescue, where they use their Digivices to free Leomon from the Black Gears. Leomon later explains the prophecy that the children, as "DigiDestined", are to the saviors of the Digital World. The group fights Devimon, who absorbs Black Gears and Ogremon. Devimon defeats the DigiDestined, even when Joe and Sora rejoin them. Patamon Digivolves into Angemon when T.K. is in danger and sacrifices himself to defeat Devimon. Angemon's data reconstitutes into a DigiEgg, and File Island begins to reform itself. The DigiDestined are then suddenly contacted by Gennai.

While the rest of the DigiDestined distract Etemon's forces, Tai and Izzy infiltrate the pyramid to save Sora, where Datamon plans on cloning her to use her Crest and Biyomon to enact revenge on Etemon. Tai musters his courage and saves Sora while Datamon activates the Dark Network to absorb data, including Etemon. Etemon, fused with the Dark Network, fights the DigiDestined, but Tai's Crest allows Greymon to Digivolve into MetalGreymon. When Etemon is defeated, a portal swallows him while Tai and Koromon are sent to Tokyo.

Tai and Koromon arrive home, where they meet Tai's younger sister, Kari, and also learn that not much time has passed since they were in the Digital World. Later, Tai gets a message from Izzy telling him not to return, and he discovers that Digimon are appearing in the Real World. He concludes that they must return to the Digital World and help their friends. After Koromon Digivolves to Agumon to battle an Ogremon, a portal opens and transports both of them back to the Digital World.

Joe's tag leads the DigiDestined to a coliseum, where Etemon traps them and forces Greymon to fight another Greymon. After Joe finds the Crest of Reliability, the group escapes and Tai forces Greymon to Digivolve to his ultimate form by putting himself in harm's way. Instead, Greymon Dark Digivolves into SkullGreymon, attacking everyone before eventually reverting to a regretful Koromon.

After T.K. finds the Crest of Hope, Izzy receives an e-mail from Datamon, who asks them to rescue him from Etemon's pyramid in exchange for Sora's Crest. Tai, Sora, Izzy, and Joe infiltrate the pyramid, with Tai being overconfident that the Digital World is a virtual reality. However, once Datamon is freed, he kidnaps Sora and Biyomon. Tai becomes too frightened to pursue Datamon after Izzy warns him that they could die.

The kids meet the ruler of File Island, Devimon, the controller of the Black Gears.

While at camp, Tai, Matt, Sora, Izzy, Mimi, Joe, and T.K. come across seven Digivices and are transported to a strange Digital World where they make friends with creatures called Digimon who claim to be their chosen partners.

Matt finds Joe working at Digitamamon's diner to pay off his debt and agrees to help. DemiDevimon bribes Digitamamon to keep them while setting off accidents that makes Matt question Joe. However, once Digitamamon's scheme is exposed, they battle him with Tai and T.K. Joe sacrifices himself to save T.K., leading Matt to see him as a true friend and allowing Garurumon to Digivolve into WereGarurumon. After Digitamamon's defeat, the group splits up and continue their search for the remaining DigiDestined.

The kids stumble upon a factory where they find an Andromon in trouble.

The kids come across a beach with numerous phone booths, but none of them seem to work.

The kids run away from a Monochromon battle. They come across a trolley car on a small island and decide to spend the night in it, until they are attacked by a Seadramon.

When the group is attacked, Tai and Agumon are hesitant to fight since Digivolving into SkullGreymon. Piximon rescues and trains the DigiDestined at his facility, where Tai and Agumon are stranded in a cave as the others do manual labor. At night, Matt and Izzy sneak away to find the Crest of Friendship and the Crest of Knowledge. However, they are detected by the Dark Network as Etemon sends a Tyrannomon after them. Tai and Agumon regain the courage to fight, leaving to Agumon Digivolve into Greymon and defeating Tyrannomon.

Tai and Agumon return to the Digital World to find Tokomon, who reveals that everyone has split up to find them after weeks since their disappearance. Meanwhile, DemiDevimon causes a rift between T.K. and Tokomon and secretly plans on feeding T.K. amnesic mushrooms. Agumon exposes DemiDevimon, and Tokomon Digivolves into Patamon to drive DemiDevimon away.

Izzy falls into Vademon's pocket dimension and is forced to give up his curiosity. Tentomon snaps Izzy out of his trance, but by that time, DemiDevimon tries to buy Izzy's Crest from Vademon. In the confusion, Izzy recovers his Crest and his curiosity as he causes Kabuterimon to Digivolve into MegaKabuterimon, defeating Vademon. Izzy and Motimon are found by Matt and T.K. soon after.

Tai and Agumon land on a snow-covered island and are forced to defeat a Frigimon.

On Server, the DigiDestined arrive at a Koromon village, only to find Pagumon living there. Despite the Pagumon's warm welcome, they are allied with Etemon and abduct Tokomon at night, imprisoning him with the Koromon. The DigiDestined rescue them, but Etemon uses his Dark Network to defeat them and destroy the village. The group take refuge in a cave, where Tai finds the Crest of Courage, allowing them to escape from Etemon into the desert.

Tai and Matt argue whether they should climb Infinity Mountain. Joe and Gomamon decide to climb the mountain by themselves. While on the mountain, they are attacked by a Unimon.

After an encounter with Ogremon at sea, Joe and Gomamon find themselves on an island with Sora and Biyomon before they are captured by a cult of Bakemon intent on eating them. Gomamon and Biyomon manage to escape and Digivolve to fight Lord Bakemon. Joe uses a Buddhist mantra to weaken Lord Bakemon. After Birdramon and Ikkakumon destroy Lord Bakemon, they ride across the sea to find their friends.

Gennai urges the group to travel to Server in order to defeat another enemy, informing them about Crests, which will allow their Digimon to Digivolve even further. While traveling on the ocean, the DigiDestined are swallowed up by Whamon, who is under the control of a Black Gear. Tai frees him with his Digivice, and as gratitude, Whamon takes the DigiDestined into an undersea store where the Crest tags are located. They fall under attack to Drimogimon and free him from a Black Gear. After recovering the tags, Whamon proceeds to take them to Server.

After getting lost in the desert, the group is taken aboard a ship traveling in the desert, headed by Kokatorimon. Kokatorimon captures all the boys and petrifies their partners. Biyomon and Palmon Digivolve and defeat him, and his ship crashes into a giant cactus. Mimi finds the Crest of Sincerity on top of the cactus.

Tai and Joe find Mimi with the Gekomon and Otamamon, who treat her like a princess hoping that her singing voice will awaken ShogunGekomon. However, Mimi becomes too consumed in being pampered to give it up and imprisons Tai and the others after they attempt to record her voice. After a nightmare, Mimi apologizes and awakens ShogunGekomon. ShogunGekomon, however, attacks Mimi, causing MetalGreymon to defeat him.

The kids come to a Yokomon village to rest for the evening until a Meramon attacks.

Mimi and Palmon escape Sukamon and Chuumon and cross over to the next island where Izzy and Tentomon landed, but end up getting lost in a labyrinth and attacked by Centarumon.

While escaping the Numemon who attacked the group in the sewers on their way out of the factory, the kids are split up and Mimi ends up in Toy Town.

T.K. and Patamon arrive in Primary Village, the place where all Digimon are born. When the baby Digimon start to cry, T.K. and Patamon are confronted by Primary Village's caretaker, Elecmon, which they settle with a tug-o-war match. Patamon wins and earns Elecmon's respect and trust, as he allows the both of them to stay. Meanwhile, Devimon sends Leomon after T.K, considering him a threat.