When BlackWarGreymon destroy the third stone, a digimon briefly appears and BlackWarGreymon becomes convinced that this is his worthy opponent. At the next site, despite Angemon digivolving to MagnaAngemon after he touches the Stone, the Destined lose the battle. Gabumon tells the children about Agumon's discussion with their foe.

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. Ken brings her Poromon, who helps her to combat the digimon until they are suddenly brought back to the Digital World.

BlackWarGreymon has a discussion about life with Agumon. Arukenimon and Mummymon turn their attention to the fabled Destiny Stones, damaging one with Knightmon (another creation of Arukenimon) and somehow causing BlackWarGreymon great pain in the process.

While searching for Gatomon's tail ring, Yolei, Kari, Ken, and their Digimon stumble into the Dark Ocean. When they are attacked by Blossomon, another of Arukenimon's creations, Gatomon and Aquilamon DNA digivolve into Silphymon.

While Cody's doubts towards Ken causes Ken to leave the group, Mummymon and Arukenimon combine a hundred control spires to create BlackWarGreymon. Even after Yolei brings Ken back to the group so they could form Paildramon, BlackWarGreymon effortlessly defeats the DigiDestined, but refuses to finish the job, and instead leaves Mummymon and Arukenimon, to search for a "worthy opponent."

The group travels once again to the Digital World only to be attacked by the Digimon Emperor. As they hide from him, T.K. and Kari discover their own Digi-Eggs, which allow Gatomon and Patamon to armor digivolve into Nefertimon and Pegasusmon.

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. As the gang is about to defeat her, another digimon, Mummymon, sweeps in to save her.

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. When they find the spider woman, however, she uses her flute to take control of Stingmon and Digmon as well.

Paildramon and Okuwamon continue fighting. Ken puts his crest of kindness into a slot in the base, but it does not do anything. Paildramon destroys the base entirely, and Izzy explains DNA digivolving and the story of how the original DigiDestined gave up the powers of their crests, which is why their Digimon can't digivolve to ultimate level anymore.

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. Suddenly, ExVeemon and Stingmon DNA digivolve to Paildramon.

The strange woman changes control spires into digimon. She turns one into a Golemon who tries to destroy a dam where Mimi and Palmon are. The DigiDestined cannot destroy Golemon and are forced to get Ken and Stingmon's help to destroy Golemon. Once Palmon wakes up and reveals that Golemon is a fake digimon, which is deduced as the reason behind Ken's actions, Yolei is able to get Hawkmon to digivolve into Aquilamon and helps destroy Golemon.

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. Ken sees a strange woman in his room that won't tell him her name. When a mysterious digimon who is Stingmon, Wormmon's evolved form destroys Thundermon, it leads the DigiDestined to question Ken's behavior.

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). He goes looking for Wormmon, and finds his baby form, Leafmon, in Primary Village.

Davis, in an effort to catch Kari's attention, wants Veemon to evolve like Patamon. His effort only manages to anger a Tortomon that chases them across the land. Veemon digivolves to ExVeemon to fight him off.

Kimeramon and Magnamon fight. Ken's base explodes, and Wormmon gives all the power he has to help Magnamon defeat Kimeramon. Kimeramon dies, and Ken gets upset because Wormmon is dead like his older brother, Sam. Davis finds the Crest of Kindness on the ground and gives it to Ken.

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.

Cody, Yolei, Davis, T.K, Kari, Izzy and Sora go to the Digital World. Yolei and Cody get their partners (Hawkmon and Armadillomon). Davis and Veemon get captured by the Digimon Emperor, and the others must save him.

All of the new DigiDestined (except Davis, who can't fly to the location) sneak into Ken's base. Ken goes into the Dark Whirlpool, even through Wormmon told him not to. Devimon comes out, and T.K. gets mad because of what he did to Patamon long ago and fights Ken. When Ken escapes T.K., he releases Kimeramon on the DigiDestined, and they must flee.

The DigiDestined decide to remain in the Digital World until they locate Ken's base, with Tai, Matt, and Izzy on a camping trip with Matt's dad as a cover story for their trip. Yolei's recklessness causes Hawkmon to be hurt. Kari and Gatomon stay behind with her. Meanwhile, Ken works on creating a digimon named Kimeramon.

Both the old and new DigiDestined gather to celebrate the anniversary of the day they first went to the Digital World, but the TV Network has problems with their cameras and claim there is a ghost haunting the TV System. All the DigiDestined discover the ghost is really Wizardmon. Wizardmon tells them a cryptic message before vanishing.