Myotismon surrounds Odaiba in fog and has his followers capture all families living in the city. Among the prisoners, Sora and Mimi try to plan an escape, using Joe's Buddhist mantra to weaken the Bakemon. However, Phantomon is unaffected and DarkTyrannomon overpowers Togemon. After Togemon Digivolves into Lillymon to tame DarkTyrannomon, she finds herself facing Myotismon while Biyomon Digivolves into Birdramon to drive off Phantomon.

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.[Note 4] Angered, WereGarurumon and Angemon drive Myotismon away.

With Wizardmon's help, Gatomon discovers that Kari is the eighth child and she is her partner. Entrusting Kari's Digivice to Tai, Wizardmon and Gatomon infiltrate Myotismon's lair to steal the Crest of Light. Myotismon catches them in the process and discovers the truth as well, throwing Wizardmon into the ocean while holding Gatomon captive.

Sora escapes, but Mimi is recaptured, while Izzy heads to Fuji TV Station. Joe and T.K. travel back through Odaiba Bay and find Wizardmon, but they are attacked by MegaSeadramon, who is defeated by Ikkakumon's ultimate form, Zudomon. Tai entrusts Kari to Matt before heading towards the convention center, but Phantomon follows Sora to them. Kari sacrifices and reveals herself as the eighth child in exchange for their safety.

VenomMyotismon is defeated after he exposes his weak point, which WarGreymon and MetalGarurumon exploit. The fog clears to reveal the Digital World reflected in the sky, and the DigiDestined realize that the boundaries between both worlds have begun to intersect, as years have passed in the Digital World since their departure. The DigiDestined decide to return to the Digital World, leaving their families.

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.

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 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 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. At 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,[10][Note 3] who later accidentally pushes Izzy off a bridge. After Ikkakumon defeats Gesomon at the ocean, he carries the DigiDestined home.

While DigiDestined continue their search for the eighth child, Sora and Mimi head to Tokyo Tower and encounter SkullMeramon, battling him. Tai and Izzy come to their aid, with Greymon Digivolving to MetalGreymon and defeating him while Kabuterimon saves the Tower. Meanwhile, Gatomon meets Kari and realizes that she is unable to kill her.

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 attempt to escape by sea, but they are immediately stopped by MetalSeadramon.

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.