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.

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.

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

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 Digital World falls under attack from the Digimon Emperor, and the Digimon are unable to Digivolve. When Kari Kamiya, T.K. Takaishi, and their classmate, Davis Motomiya, enter the Digital World to save Tai Kamiya, Davis lifts the Digi-egg of Courage and meets Veemon, who is able to Armor Digivolve into Flamedramon and save them from an enslaved Monochromon

Kimeramon and Magnamon fight. Ken's base explodes, and Wormmon gives all the power he has to help Magnamon defeat Kimeramon.

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.

Ken reminisces about his brother Sam, his digivice, an e-mail he got, and when he first went into the Digital World (despite his temporary amnesia in the real world).

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.

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 see that Ken's base is about to explode. Okuwamon, a digimon made from control spires, attacks the DigiDestined. Ken comes, and Davis talks about friendship.

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

The DigiDestined arrive at the giant Giga House, where the strange woman lies in wait. As they draw closer to her, the group is attacked by different kinds of insect digimon.

Yolei creates a counter to the strange woman's music (because she worked with Matt's band). She transforms into a Digimon called Arukenimon and a fight breaks.

While Cody's doubts towards Ken causes Ken to leave the group, Mummymon and Arukenimon combine a hundred control spires to create BlackWarGreymon.

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

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.

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

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.

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

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.

All of the new DigiDestined (except Davis, who can't fly to the location) sneak into Ken's base.

Kimeramon soundly defeats the DigiDestined. Wormmon leads Davis and Veemon to the power source of the base. It turns out to be a golden Digi-egg, which Davis uses to golden armor digivolve Veemon to Magnamon.

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.