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.

A MegaSeadramon gets the DigiDestined stuck under an oil platform. Cody admits to being afraid of water, so the others force Cody to get help to overcome his fear. He finds Joe, and they come back to save the rest of the group, who found the Digi-Egg of Reliability, Cody's second Digi-Egg. Cody can't accept the egg because he lied to his grandfather. But thanks to a pep talk from Joe about some lies that can be helpful, Cody overcomes his self doubt and ends up using the Egg. At the end, Submarimon gives Cody a tour of the sea.

The DigiDestined travel to a town out of the Japanese Edo period. While fleeing the controlled Floramon and Mushroomon, they meet the ruler, ShogunGekomon. Shortly after, Ninjamon puts a spiral on ShogunGekomon and the DigiDestined must stop the rampaging digimon.

The new DigiDestined eat at a diner. The owner of the shop, Digitamamon, becomes angry because they do not have any money. Michael and Mimi come into the diner and pay the bill. Later, Digitamamon ends up controlled by a Dark Spiral and hurts Mimi. Yolei activates the Digi-Egg of Sincerity (after finally giving Digitamamon the benefit of the doubt and promising to be sincere) to free the ultimate-level.

Kari is dragged into a world that is neither the real world nor the Digital World. T.K., Gatomon, and Patamon follow her, and together they are able to defeat Airdramon and destroy the Control Spire. However, the Digimon that brought Kari into their world warn her that their master will later come for her.

Biyomon goes missing and the teams ends up in a town straight out of a cowboy film. Starmon, under the control of Ken, puts the DigiDestined in jail, where they find the captured rookie. The girls of the group are promptly freed by Deputymon to go and play cards with him. Soon after, though, the boys manage to break out and destroy the Control Spire.

Just after finding a new Digi-Egg, the DigiDestined are attacked by Flymon and MetalGreymon, under the control of the Emperor's improved Dark Spiral. Davis eventually manage to activate the egg (after confirming his friendship to Veemon). Veemon armor digivolves to Raidramon and destroys the spiral.

Ken, angry at his inability to control SkullGreymon, works on his Dark Ring. Wormmon, in the hope that Ken might use him in his experiments, frees Agumon. However, as he reunites with Tai, Ken captures him with his new Dark Spiral, and makes him dark digivolve into MetalGreymon and attack the DigiDestined.

The digital adventure continues as three new DigiDestined (Davis, Yolei, and Cody), receive their digivices and Davis meets Veemon, his partner. Veemon armor digivolves into Flamedramon to fight off a Monochromon being controlled by the evil Digimon Emperor.