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.

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

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

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.

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.

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

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

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 ghost-based Digimon named Bakemon intent on eating them.

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-of-war match.

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 legend of the "DigiDestined", a group of children from another world who will save the Digital World from evil forces.

Gennai urges the group to travel to Server to defeat another enemy. Gennai also tells about Crests that will allow Digimon to digivolve further. The kids build a raft and leave File Island and are taken by Whamon to where the Crests are hidden.

The kids arrive in a Koromon village where they are confronted by Etemon. 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.

While traveling in the desert the group is trapped by Etemon in a coliseum.

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.

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.

After Izzy receives an e-mail from Datamon, who asks them to rescue him from Etemon's pyramid in exchange for Sora's Crest, T.K. finds the Crest of Hope. 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.

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.

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.

Matt, Gabumon, Joe, and Gomamon are forced to work at Digitamamon's diner to pay off a meal.

Izzy is trapped in Vademon's pocket dimension and robbed of his curiosity. DemiDevimon attempts to buy Izzy's Crest from Vademon and, in the confusion, Izzy recovers his Crest and his curiosity.

Joe and Tai find Mimi being treated like a princess at a palace. Sora convinces her to sing and awaken ShogunGekomom, but ShogunGekomom attacks the kids.

The DigiDestined find Sora, realizing that she had been helping them in secret. Sora is convinced by DemiDevimon that her Crest would never glow, recalling her relationship with her mother. That night, Myotismon appears, defeating the Digimon. Sora tries to stop an injured Biyomon from fighting for her well-being and realizes that her mother's actions towards her were the same. Birdramon is able to Digivolve into Garudamon, and the DigiDestined escape.

Gennai appears and tells them that there is an eighth DigiDestined and that Myotismon is planning to go to the Real World with an army of evil Digimon to find the child. The DigiDestined infiltrate Myotismon's castle to stop him entering the Real World, but they fail when Gatomon distracts them with Devidramon.

The DigiDestined travels to Gennai's home, where he unravels secrets about the Digital World. They return to Myotismon's castle to open the gate and battle Dokugumon. The fight causes the castle to crumble as WereGarurumon destroys Dokugumon, but they manage to open the gateway and escape through it.

The DigiDestined find themselves back at camp, learning they were only gone for a few minutes. They proceed to head towards Highton View Terrace to try to find the eighth child. There, a battle between Garudamon and Mammothmon helps them recall them witnessing a battle four years ago between a Greymon and a Parrotmon. They surmise that the eighth child must have also seen the fight.

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, who later accidentally pushes Izzy off a bridge. After Ikkakumon defeats Gesomon at the ocean, he carries the DigiDestined home.

After the DigiDestined return home, the eighth child's Digivice gets carried off by Tai's cat and sets off a signal that brings in DemiDevimon, Raremon and Izzy. Kabuterimon manages to defeat Raremon, but Izzy and Tentomon's search leads them to no results.

The DigiDestined continue their search for the eighth child. Gatomon crosses paths with Kari and wonders if she could be the eighth child.

T.K. and Patamon get into a fight on their way home, and when Patamon flies off, Matt and T.K. follow him into Shibuya. They encounter Pumpkinmon and Gotsumon, who are more interested in having fun rather than helping Myotismon. When they refuse to fight Matt and T.K., Myotismon punishes them. Angered, WereGarurumon and Angemon drive Myotismon away.

Wizardmon finds Kari's Digivice and brings Gatomon and Kari together. It is revealed that Kari is the eighth DigiDestined child and that Gatomon is her partner.

Myotismon creates a barrier of fog around Odaiba and evil Digimon roam the streets. Bakemon and Phantomon begin taking people from their homes and holding them prisoner.

Myotismon uses Gatomon to try and identify the eighth child. Kari is found by Phantomon and gives herself up so that Matt and Sora are not harmed.

The DigiDestined reunite at Fuji TV Station to fight Myotismon and Phantomon. Myotismon tries to kill Kari and Gatomon, Wizardmon sacrifices himself to protect them. Distraught, Kari causes Gatomon to Digivolve into Angewomon, destroying Myotismon with a combined attack. However, fog still remains around Odaiba.

Myotismon is reborn as VenomMyotismon, empowering himself by consuming his army before advancing to the convention center for the humans. Recalling Gennai's prophecy from earlier, Izzy discovers that Angemon and Angewomon must strike Tai and Matt in order to bring about a miracle that will allow them to defeat VenomMyotismon. Tai and Matt risk their lives and fulfill the prophecy, allowing Agumon and Gabumon to Warp Digivolve into WarGreymon and MetalGarurumon.

With the help of the entire team and their Digivices, WarGreymon and MetalGarurumon are able to defeat VenomMyotismon. However, immediately following the battle they must leave for the Digital World, which is once again in danger.

As the DigiDestined return to the Digital World, they encounter Chuumon, who tells them that the Dark Masters have taken over the Digital World while they were in Tokyo. The DigiDestined face the Dark Masters, who overpower their Digimon, and Chuumon sacrifices himself to protect Mimi. Pixiemon arrives to save the DigiDestined, sacrificing himself to allow them to escape.

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

Just as the kids are about to be destroyed by MetalSeadramon, Whamon comes to their rescue and they flee to the bottom of the ocean. However, when MetalSedramon catches up to them, a battle begins.

Whamon sacrifices himself while saving WarGreymon, allowing WarGreymon to defeat MetalSeadramon. The DigiDestined proceed to Puppetmon's forest, where he separates them, causing Matt to become overprotective of T.K. Puppetmon forces T.K. to play deadly game of hide-and-seek in exchange for the DigiDestined's safety, but T.K. tricks him and sabotages his control room. After the other DigiDestined regroup and defeat Kiwimon, Matt becomes discouraged seeing that T.K. has escaped without his help.

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.

Tension runs high as a fight breaks out between Matt, Tai, and their Digimon. Kari's body is taken over a strange entity, who explains why the DigiDestined were chosen to save the Digital World. Uncertain, Matt leaves the group. Upset from the conflict, Mimi leaves as well, with Joe accompanying her. The rest of the DigiDestined continue their journey to fight the Dark Masters.

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.

SaberLemon rescues Joe and Mimi, but they are found by MetalEtemon again. He destroys MetalEtemon with Joe and Zudomon's help but dies from a fatal wound from protecting Mimi. At the same time, Puppetmon is defeated by the DigiDestined and destroyed by Matt and MetalGarurumon upon escaping. Recognizing Puppetmon's defeat and Leomon's sacrifice, Mimi regains her will to fight as she and Joe decide to gather more reinforcements while Tai's group fights the remaining Dark Masters.

Kari falls ill, and Tai becomes nearly hysterical in his attempts to help her. Machinedramon attacks them in a mechanical city under his control, and the group is separated.

Separated in the sewers, the DigiDestined must reunite while under attack.

As Joe goes off on his own to find Matt, Tai's group encounters LadyDevimon, one of Piedmon's servants. Sora and T.K. are sent to locate the rest of the missing DigiDestined while Angewomon and MegaKabuterimon face and defeat LadyDevimon. After LadyDevimon's defeat, Piedmon approaches the group.

Piedmon and WarGreymon battle, but WarGreymon cannot stop him alone. Matt falls into a dark cave, but he escapes once he confronts his feelings. After rescuing Sora from her dark cave, they return with Joe. Matt makes up with Tai, activating the Crest of Friendship. With all of the DigiDestined but Mimi reunited, both WarGreymon and MetalGarurumon prepare to battle Piedmon.

Piedmon turns the DigiDestined and their Digimon into doll keychains. With T.K. and Kari remaining, T.K. imagines Matt giving him advice, regaining hope and activating his Crest. Angemon Digivolves into MagnaAngemon and saves the rest of the DigiDestined, and together, they defeat Piedmon when Mimi reunites with the group. The DigiDestined are unable to celebrate their victory when they receive an e-mail from Gennai, who reveals that another enemy is the true cause for the destruction of the Digital World.

Although the Dark Masters are defeated, it is not enough to stop the complete destruction of the Digital World and the children and their Digimon are forced to face the true mastermind of all the chaos - Apocalymon.

Apocalymon is defeated, and the DigiDestined prepare to spend the rest of their summer in the Digital World. However, Gennai informs them that they either have to leave quickly, or remain in the Digital World forever.