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.
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.
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.
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. They meet Palmon, but are then attacked by the Roachmon brothers, Gekomon and Otamamon, who are under the Digimon Emperor's control.
After trying to destroy a control spire located in a city, Kari is separated from the rest of the group. Davis and T.K. return to rescue her. Kari eventually manages to free Andromon from the dark ring's control.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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, 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.
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.
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, Stingmon and ExVeemon DNA-digivolve to Paildramon.
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 DigiDestined arrive at the giant Giga House, where Arukenimon 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.
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 (only after Yolei slaps Kari in the face, something Kari did earlier in the episode).
BlackWarGreymon has a discussion about life with Agumon. Arukenimon and Mummymon turn their attention to the fabled Destiny Stone, destroying one and somehow causing BlackWarGreymon great pain in the process.
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.
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.
The DigiDestined head out to eat at another Digitamamon restaurant. Arukenimon and Mummymon are already there, badgering the digimon to tell them what his soup recipe is. When he refuses, they look for themselves, and discover the final destiny stone in the soup springs. When BlackWarGreymon shows up, Angemon and Ankylomon DNA digivolve into Shakkoumon, and the episode ends.
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, the digimon that appeared as earlier destiny stones were destroyed. BlackWarGreymon attacks Azulongmon but quickly is shoved off and leaves after learning what his purpose is. After explaining many such things as the true purpose of the control spires and armor digivolving, Azulongmon warns the group about their true enemy, the one controlling Arukenimon and Mummymon. Davis sees a control spire in ...
As Christmas approaches, the DigiDestined take on a festive mood. Ken goes so far as to throw a party (the first time he was truly happy in a long time). The younger group brings the digimon partners of the original DigiDestined into the real world. However, their holiday cheer ends when control spires and rampaging digimon appear worldwide.
The DigiDestined receive one of Azulongmon's Digicores, which results in Paildramon mega digivolving into Imperialdramon Dragon Mode, who helps them to join the other DigiDestined worldwide. It also restores the original 8's ability to go to ultimate level.
Ken and Matt help out the a Mexican DigiDestined, while Sora and Yolei helped those in Russia and Siberia. They all return back to Japan, just in time for Christmas. However, Arukenimon is still up to something.
A new enemy, Daemon, appears, along with his followers. With the aid of Azulongmon's power given up by the older digimon, Imperialdramon Dragon Mode triumphs against SkullSatamon by mode changing into his Fighter Mode!
Yukio Oikawa and his cronies kidnap Ken, and use his Dark Spore to create new ones to implant in gathered children. Meanwhile, Daemon's servants engage the DigiDestined, and, in order to win, the DigiDestined must kill both of them.
Oikawa, having no more use for Ken, attempts to hand him off to Daemon, however, Davis intervenes. The other DigiDestined arrive, and with their help, Ken is able to open a gate to the Dark Ocean and send Daemon through it.
BlackWarGreymon confronts Oikawa, who tells him the truth about his creation. The digimon tries to destroy Oikawa, but is stopped by both WarGreymon (which was the result of another power boost Agumon received from Azulongmon) and Imperialdramon Fighter Mode. After a fierce battle, they plead with BlackWarGreymon to befriend them.
One of the children's Dark Spores grows into a Dark Flower, which is harvested by Oikawa despite the DigiDestined's best efforts to stop him. Cody's grandfather tries to convince Oikawa to give up villainy, but fails. Before Oikawa can kill him, however, BlackWarGreymon takes the fatal blast. The dying mega uses the last remnants of power to seal the digital gate at Highton View Terrace.
Oikawa and the children infected with the Dark Spores try to go to the Digital World, but, due to BlackWarGreymon's sealing of the gate, travel to a different world, where MaloMyotismon, who had hidden within Oikawa ever since his defeat, makes his appearance.
The six DigiDestined, assisted by DigiDestined all over the world and Oikawa's gathered children, destroy MaloMyotismon. Oikawa is left dying in the dream dimension and uses the power of the dimension to help restore the Digital World to its original state. Twenty-five years later, when everyone in the Real World has a Digimon partner, both groups of DigiDestined are grown and their children now hold the responsibility of protecting the worlds.