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.
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.
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.
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 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.
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.
As Davis joins up with Mimi and the American DigiDestined, Kari and Izzy receive help from the Poi Brothers in Hong Kong.
Cody, worried about T.K., visits Matt, who tells him that T.K. still carries the scars from the battle against Devimon. Determined to stop BlackWarGreymon, Cody personally fronts him. However, BlackWarGreymon is won over by his instincts and destroys the fifth Destiny Stone.
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.
Yolei neutralizes the woman's flute music, and the woman reveals herself as Arukenimon. Arukenimon is defeated, but she is rescued by Mummymon and they escape.
The DigiDestined head to Giga House to find the woman, only to find out that her flute music has put all the insect Digimon under her control, including Stingmon and Digmon.
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.
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.
MegaSeadramon traps the DigiDestined under an oil platform, and Cody is forced to find Joe, lying in the process. When they return, the DigiDestined find the Digi-egg of Reliability, which Cody is reluctant to accept due to lying. However, Joe convinces him to overcome his self-doubt and Cody allows Armadillomon to Armor Digivolve into Submarimon, freeing MegaSeadramon.
The DigiDestined travel to a town out of the Japanese Edo period. While fleeing the controlled Floramon and Mushroomon, they meet their ruler, ShogunGekomon. Shortly after, Ninjamon puts a spiral on ShogunGekomon and the DigiDestined must stop him.
Biyomon sends a distress call, and the DigiDestined accompany Sora to a Western town, where Starmon arrests them. Deputymon frees the girls only to entertain him and gets into a confrontation with Starmon. while the boys escape. Flamedramon defeats Starmon and sends him flying into the Control Spire, destroying it.
When the DigiDestined find the Digi-egg of Friendship, they are attacked by Flymon and MetalGreymon. Davis is conflicted about fighting Agumon at first, but once he realizes he needs to protect his friends, the Digi-egg of Friendship activates and allows Veemon to Armor Digivolve into Raidramon.
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.
Gabumon is captured and tortured by an enslaved RedVegiemon for helping the Gazimon rebel. With Matt Ishida, the DigiDestined rescue Gabumon and inadvertently destroy a Control Spire, allowing Gabumon to Digivolve again and freeing the Digimon Emperor's slaves.
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.
When Yolei Inoue and Cody Hida enter the Digital World with the DigiDestined, Davis and Veemon are captured. Under Sora Takenouchi and Izzy Izumi's advice, Yolei and Cody pick up the Digi-eggs of Love and Knowledge and meet Hawkmon and Armadillomon, allowing them to Armor Digivolve into Halsemon and Digmon to save them.