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.

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.

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.

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.

Assisted by DigiDestined all over the world and the kidnapped children, the DigiDestined weaken MaloMyotismon with their dreams and Imperialdramon destroys him, ending Myotismon’s reign of terror for good. Oikawa sacrifices himself by using the power of the Dream World dimension to become data and restoring the Digital World. Twenty-five years later, everyone in the Real World has a Digimon partner, and the DigiDestined's children hold the responsibility of protecting the worlds.

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.

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.

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.

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.

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.

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.

During Kimeramon and Magnamon's fight, Wormmon sacrifices his life energy to give Magnamon the strength to defeat Kimeramon. Wormmon dies, and Ken is forced to accept that the Digital World was real while facing his past. The Digi-egg of Miracles disintegrates into the Crest of Kindness for Ken, and with the Digimon Emperor gone, the DigiDestined return home.

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.

MaloMyotismon tempts the DigiDestined with illusions of their dreams, but Davis, whose dream was that ExVeemon could grow more powerful to defeat him, guides them out. The others follow his example, causing the Digimon to duplicate all Digivolutions. The attacks of all the Digimon send MaloMyotismon into the Digital World, leaving only Imperialdramon, Silphymon and Shakkoumon to face him, as he increases his powers.

One of the children's Dark Spores blooms into a Dark Flower and is harvested by Oikawa, despite the DigiDestined's best efforts to stop him. When Cody's grandfather fails to dissuade him, BlackWarGreymon sacrifices himself to protect him. Noticing that Oikawa is possessed, he uses his remaining power to seal Highton View Terrace's portal to the Digital World.

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.

In a dream, Ken reminisces entering the Digital World for the first time and becoming resentful towards his older brother, Sam. When Sam dies, Ken receives an e-mail leads him to becoming the Digimon Emperor. After waking up, Ken returns to the Digital World and ends up in Primary Village where, after promising to redeem himself, he is reunited with Wormmon in his infant form Leafmon.

When BlackWarGreymon destroys the third Destiny Stone, he is convinced that he is destined to fight the Digimon that appears when a Destiny Stone is destroyed. The DigiDestined realize that destroying all the Destiny Stones would upset the balance between all worlds. T.K. becomes frustrated, and despite Angemon digivolving to MagnaAngemon, BlackWarGreymon still destroys the next Destiny Stone.

With the Digimon Emperor's base about to explode, the DigiDestined try to contain it, only to be confronted by the woman creating Okuwamon from ten Control Spires. While Ken comes to their aid, he wants to deal with the crisis himself out of atonement, but Davis refuses to allow this. Davis' declaration of friendship causes ExVeemon and Stingmon to DNA Digivolve into Paildramon.

Davis and Yolei make a failed attempt at improving Cody and Ken's relationship. Arukenimon creates BlackWarGreymon from 100 Control Spires to fight against the DigiDestined, and he overpowers their Digimon. However, BlackWarGreymon rebels against Arukenimon and Mummymon, leaving them.

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.

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.

Paildramon fights Okuwamon while the DigiDestined enter Ken's base, and Ken putting the Crest of Kindness into the energy core is ineffective. However, once Paildramon defeats Okuwamon, he destroys the remains of the base as well. The next day, the DigiDestined meet with Izzy, who explains DNA Digivolution and the original DigiDestined's sacrifice to protect the Digital World years ago.

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.

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.

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

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.

As the Digimon fight BlackWarGreymon, the DigiDestined attempt to move the Destiny Stone with their D-3s under Davis' advice. This summons Azulongmon, who had appeared when the Destiny Stones were destroyed. BlackWarGreymon is defeated by Azulongmon and leaves to look for his life's purpose. Azulongmon explains to the DigiDestined about Control Spires and Armor Digivolution, while warning them that Arukenimon is not their true enemy.

With Oikawa's goal complete, he hands Ken over to Daemon. Davis and the other DigiDestined intervene, but Imperialdramon and the other Digimon are powerless against him. As Daemon is able to re-enter the Real World even after being sent back to the Digital World, Ken takes a risk in redirecting the portal to the Dark Ocean. Oikawa lets the kidnapped children return home as he and his followers escape.

After summer vacation ends, the DigiDestined return to the Digital World to help the Digimon with reconstruction. While there, Davis, in an effort to impress Kari, wants Veemon to Digivolve naturally like Patamon. Instead, he angers a Tortomon, who chases them. Veemon Digivolves to ExVeemon to fight him.

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.

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

While the DNA digivolved digimon hold off BlackWarGreymon, Davis gets the idea of moving the last Destiny Stone with the D3s. Instead of moving it, this summons Azulongmon.

Cody, worried about T.K., goes to see Matt, who tells him about how T.K. still carries the scars from the battle against Devimon. BlackWarGreymon destroys one of the final two destiny stones.

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.

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.

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.

Ken and Matt help out a Mexican DigiDestined, while Sora and Yolei helped those in Russia and Siberia. Yolei and Sora are successful in Russia, but they are rescued from an attack by Imperialdramon. The DigiDestined return home in time for Christmas, but while they were traveling, Arukenimon and Mummymon have been gathering children.

Davis, Kari, and T.K. find that their Digimon can't Digivolve. Cody is attacked by Thundermon, leading to Armadillomon's unexpected digivolution into Ankylomon.

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

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

When BlackWarGreymon destroy the third stone, a digimon briefly appears and BlackWarGreymon becomes convinced that this is his worthy opponent.

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.

In Australia, Cody and Joe meet with Derek to fight marine Digimon. In Paris, T.K. and Tai receive help from T.K.'s grandfather to save a French DigiDestined held hostage in Versailles by the Mamemon brothers.

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.

The DigiDestined find Arukenimon and Mummymon at Digitamamon's Chinese restaurant and discover that the final Destiny Stone is hidden in the restaurant's springs. When BlackWarGreymon appears, Angemon and Ankylomon DNA Digivolve into Shakkoumon, preparing to fight with the other Digimon.

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.

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

Mimi and the new DigiDestined have a picnic in the Digital World. But Mimi falls into a hole and, along with Yolei, is separated from the rest of the DigiDestined.

The DigiDestined are attacked by Tyrannomon. T.K. and Kari find the Digi-eggs of Hope and Light, allowing Patamon and Gatomon to Armor Digivolve into Pegasusmon and Nefertimon to save their friends and free Tyrannomon.

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.

Yolei, while on a school trip, encounters BlackWarGreymon and several other digimon in the real world after the mega just destroyed a second Destiny Stone.

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.

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.

Ken meets Yukio Oikawa, who knows his past and wants to copy the data of the Dark Spore embedded in his neck for the kidnapped children. The rest of the DigiDestined fight LadyDevimon and MarineDevimon to catch up to him. Yolei and Cody are both forced to watch their Digimon partners kill other Digimon.

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.

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

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