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.

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.

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.

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.

While Davis and Veemon remain behind, the rest of the DigiDestined infiltrate Ken's base at the Dark Whirlpool. The Dark Whirlpool contains Devimon's data, which Ken uses for Kimeramon, despite being warned about the powers of darkness. T.K. is angry upon discovering this and confronts Ken. Once Ken releases Kimeramon, T.K. escapes with the other DigiDestined and the base's prisoners.

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.

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.

Kimeramon defeats the DigiDestined, but Ken can no longer control him. Fearing for Ken, Wormmon leads Davis and Veemon to the power source of the base, the Digi-egg of Miracles. Davis uses the Digi-egg of Miracles to Golden Armor Digivolve Veemon into Magnamon.

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.

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.

Davis' soccer team plays against genius Ken Ichijoji's team. The next day, the DigiDestined fall into a trap the Digimon Emperor set up for them as he forces Davis into a compromising position in exchange for their lives. Though the Digimon Emperor's scheme is foiled, he reveals himself as Ken to Davis.

Having developed a consciousness, BlackWarGreymon comes across Agumon and seeks his advice on his purpose in life. With BlackWarGreymon refusing to obey, Arukenimon creates Knightmon to destroy one of the Digital World's Destiny Stones. Though the DigiDestined attempt to stop Arukenimon, Mummymon, and Knightmon, the damage to the Destiny Stone attracts BlackGreymon and he shatters it.

Ken flees to the Digital World to expand his territory. He captures Agumon and forces him to Dark Digivolve, resulting in the uncontrollable SkullGreymon. SkullGreymon ultimately exhausts himself and de-digivolves back to Agumon, but the Emperor escapes with him.

Kari has recurring nightmares and warps into the Dark Ocean, a world separate from the Real and Digital Worlds. The Scubamon ask Kari to free them from Ken's control, and they are attacked by an Airdramon. T.K. enters the Dark Ocean to rescue Kari and destroys the Control Spire, but once the Scubamon are freed, they attempt to abduct her into serving as their queen to their master, Dragomon. The two, along with their Digimon, escape.

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.

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.

As Davis joins up with Mimi and the American DigiDestined, Kari and Izzy receive help from the Poi Brothers in Hong Kong.

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.

After trying to destroy a Control Spire located in Fullmetal City, Kari is separated from the rest of the group. Davis and T.K. return to rescue her, but she is confronted by an enslaved Andromon. Kari convinces Andromon to fight against the Dark Ring's control and he frees himself, destroying the Control Spire.