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.

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.

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.

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.

Ken finds a woman in his room who knows his past. While helping in the restoration, Davis, Kari and T.K. find that their Digimon can't Digivolve naturally despite the Control Spires being deactivated. Cody is attacked by Thundermon, leading to Armadillomon to Digivolve into Ankylomon. Thundermon is killed by Ken and Stingmon, leading the DigiDestined to become wary of him.

Mimi and SnowBotamon are under attack when a Golemon tries to destroy a dam. With the DigiDestined unable to stop him, they are forced to seek Ken's help. Though Yolei is doubtful at first, the DigiDestined learn that Golemon was created from Control Spires by the woman. With newfound faith in Ken, Yolei causes Hawkmon to Digivolve into Aquilamon and defeat Golemon.

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.

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 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.

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.

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.