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.

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

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.

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.

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.

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.

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.

The kids manage to escape MetalSeadramon's minion, Scorpiomon. They attempt to escape by sea, but they are immediately stopped by MetalSeadramon.

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.

The DigiDestined try to get back to their homes in Odaiba after missing their train stop and spending all their money on food. Eventually they end up getting a ride from Sora's cousin Duane,[10][Note 3] who later accidentally pushes Izzy off a bridge. After Ikkakumon defeats Gesomon at the ocean, he carries the DigiDestined home.

While Puppetmon orders Garbagemon to attack the DigiDestined, Matt withdraws and meets Cherrymon. Cherrymon convinces him to defeat Tai, who he claims is the source of Matt's self-doubt. Matt returns to the DigiDestined and demands Tai to fight him, while Cherrymon is killed by Puppetmon after warning him not to underestimate an advantage that the DigiDestined have over him.

Joe and Mimi rescue an injured Ogremon, while Etemon returns as MetalEtemon to take revenge on them. Meanwhile, Tai's group infiltrate Puppetmon's mansion with the help of two of his playmates, keeping Puppetmon at bay with his own cannon.

When Yolei Inoue and Cody Hida enter the Digital World with the DigiDestined, Davis and Veemon are captured. Under Sora Takenouchi and Izzy Izumi's advice, Yolei and Cody pick up the Digi-eggs of Love and Knowledge and meet Hawkmon and Armadillomon, allowing them to Armor Digivolve into Halsemon and Digmon to save them.

Gabumon is captured and tortured by an enslaved RedVegiemon for helping the Gazimon rebel. With Matt Ishida, the DigiDestined rescue Gabumon and inadvertently destroy a Control Spire, allowing Gabumon to Digivolve again and freeing the Digimon Emperor's slaves.

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

Under attack from MetalSeadramon, Whamon comes to the DigiDestined's rescue and they flee to the bottom of the ocean. Unfortunately, MetalSeadramon and his army of Divermon find them. Whamon and Zudomon destroy the Divermon, while WarGreymon battles MetalSeadramon.

The Digital World falls under attack from the Digimon Emperor, and the Digimon are unable to Digivolve. When Kari Kamiya, T.K. Takaishi, and their classmate, Davis Motomiya, enter the Digital World to save Tai Kamiya, Davis lifts the Digi-egg of Courage and meets Veemon, who is able to Armor Digivolve into Flamedramon and save them from an enslaved Monochromon.