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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

While searching for Gatomon's tail ring, Yolei, Kari, Ken, and their Digimon stumble into the Dark Ocean.

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.

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.

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.

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.

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

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.

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.