A MegaSeadramon gets the DigiDestined stuck under an oil platform.

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.

Both the old and new DigiDestined gather to celebrate the anniversary of the day they first went to the Digital World.

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.

Sora tells the group about the meanings of their Crests and how DemiDevimon said her Crest would never glow. Myotismon appears and defeats the Digimon.

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 Kindmess for Ken, and with the Digimon Emperor gone, the DigiDestined return home.

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.

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.

Joe goes off on his own to find Matt. Angewomon faces off against LadyDevimon, one of Piedmon's servants. After LadyDevimon's defeat, Piedmon tries to approach the group.

Whamon is killed trying to help WarGreymon, who finally manages to defeat MetalSeadramon. The kids then go into a forest were they are continually taunted by Puppetmon, who uses toys to move them around.

The group travels once again to the Digital World only to be attacked by the Digimon Emperor.

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.

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.

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.

While the DigiDestined monitor the children, BlackWarGreymon confronts Oikawa, who tells him the truth about his creation, and tries to attack him. He is stopped by both WarGreymon and Imperialdramon. After a fierce battle, they plead with BlackWarGreymon to befriend them.

Oikawa attempts to bring the children to the Digital World, but because BlackWarGreymon had sealed Highton View Terrace's portal, they end up in the Dream World. Oikawa's possession manifests as Myotismon, who Digivolves into MaloMyotismon using the Dark Spores and kills Arukenimon and Mummymon. The DigiDestined become fearful, with the exception of Davis and ExVeemon.

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.

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.

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.

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.

As Davis and Ken fight Triceramon in Tamachi, the DigiDestined receive one of Azulongmon's Digicores from a rejuvenated Gennai, which results in not only restoring the original partner Digimons' ability to reach ultimate level, but also allows Paildramon Digivolve into Imperialdramon. The DigiDestined are instructed to meet Gennai's aides and the international DigiDestined worldwide to send the wild Digimon back into the Digital World.

The Daemon Corps invade Japan, targeting Ken, and SkullSatamon overwhelms Paildramon. The older DigiDestined Digimon relinquish the power to allow Imperialdramon to transform into Fighter Mode to destroy SkullSatamon. Daemon demands the DigiDestined surrender Ken, but Ken is forced to turn himself into Arukenimon's custody when she reveals the children she and Mummymon abducted.

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.

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.

Paildramon and Okuwamon continue fighting. Ken puts his crest of kindness into a slot in the base, but it does not do anything.