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.

When Yolei Inoue and Cody Hida enter the Digital World with the DigiDestined, Davis and Veemon are captured. Under Sora Takenouchi and Izzy Izumi's advice, Yolei and Cody pick up the Digi-eggs of Love and Knowledge and meet Hawkmon and Armadillomon, allowing them to Armor Digivolve into Halsemon and Digmon to save them.

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.

Gabumon is captured and tortured by an enslaved RedVegiemon for helping the Gazimon rebel. With Matt Ishida, the DigiDestined rescue Gabumon and inadvertently destroy a Control Spire, allowing Gabumon to Digivolve again and freeing the Digimon Emperor's slaves.

Gomamon is captured by the Digimon Emperor, and the DigiDestined, along with Joe Kido, plan to rescue him. On the way, Cody falls into freezing water, leaving Joe to take care of him. While the others target the Control Spire, Joe and Cody are attacked by Shellmon and Ebidramon. With the combined efforts of Digmon and Ikkakumon, the Digimon are freed.

During Golden Week, Mimi Tachikawa returns to Japan and joins the DigiDestined for a picnic in the Digital World. Yolei and Mimi are separated from the group and end up in the Night Forest, where they are attacked by the Roachmon Brothers. After they trick the Roachmon Brothers into cracking the Control Spire, Palmon is able to Digivolve into Togemon to help Halsemon defeat the Roachmon Brothers.

After trying to destroy a Control Spire located in Fullmetal City, Kari is separated from the rest of the group. Davis and T.K. return to rescue her, but she is confronted by an enslaved Andromon. Kari convinces Andromon to fight against the Dark Ring's control and he frees himself, destroying the Control Spire.

Davis' soccer team plays against genius Ken Ichijoji's team. The next day, the DigiDestined fall into a trap the Digimon Emperor set up for them as he forces Davis into a compromising position in exchange for their lives. Though the Digimon Emperor's scheme is foiled, he reveals himself as Ken to Davis.

Ken flees to the Digital World to expand his territory. He captures Agumon and forces him to Dark Digivolve, resulting in the uncontrollable SkullGreymon. SkullGreymon ultimately exhausts himself and de-digivolves back to Agumon, but the Emperor escapes with him.

Ken creates the Dark Spiral, a new version of his Dark Rings, to be able to control ultimate-level Digimon. Conflicted, Wormmon, Ken's Digimon partner, frees Agumon hoping Ken would use him for his experiments. However, as Agumon reunites with Tai, Ken recaptures him with his new Dark Spiral and makes him Dark Digivolve into a MetalGreymon's virus form and attack the DigiDestined.

Biyomon sends a distress call, and the DigiDestined accompany Sora to a Western town, where Starmon arrests them. Deputymon frees the girls only to entertain him and gets into a confrontation with Starmon. while the boys escape. Flamedramon defeats Starmon and sends him flying into the Control Spire, destroying it.

Kari has recurring nightmares and warps into the Dark Ocean, a world separate from the Real and Digital Worlds. The Scubamon ask Kari to free them from Ken's control, and they are attacked by an Airdramon. T.K. enters the Dark Ocean to rescue Kari and destroys the Control Spire, but once the Scubamon are freed, they attempt to abduct her into serving as their queen to their master, Dragomon. The two, along with their Digimon, escape.

The DigiDestined meet Mimi and Michael, an American DigiDestined, who pay for their lunch at Digitamamon's diner. Though Yolei is upset, Mimi convinces her to see Digitamamon's good side. Later, Digitamamon is enslaved by a Dark Spiral and hurts Mimi, causing Yolei to confront him and find the Digi-egg of Sincerity. Hawkmon Armor Digivolves into Shurimon and frees Digitamamon.

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

MegaSeadramon traps the DigiDestined under an oil platform, and Cody is forced to find Joe, lying in the process. When they return, the DigiDestined find the Digi-egg of Reliability, which Cody is reluctant to accept due to lying. However, Joe convinces him to overcome his self-doubt and Cody allows Armadillomon to Armor Digivolve into Submarimon, freeing MegaSeadramon.

All of the DigiDestined come together and hold a memorial for the events that took place three years ago. Meanwhile, the Fuji TV Station's cameras catch a ghost haunting area, which the DigiDestined discover is Wizardmon. Wizardmon tells them a cryptic message about how to defeat the Digimon Emperor before vanishing.

The DigiDestined decide to stay in the Digital World to find Ken's base while Tai, Matt, and Izzy plan a camping trip to avoid suspicion, only to be followed by Davis' sister, June. Meanwhile, Yolei's excitement leads into recklessness and causes Hawkmon to be injured. At night, they locate Ken's base, a flying fortress.

While Davis and Veemon remain behind, the rest of the DigiDestined infiltrate Ken's base at the Dark Whirlpool. The Dark Whirlpool contains Devimon's data, which Ken uses for Kimeramon, despite being warned about the powers of darkness. T.K. is angry upon discovering this and confronts Ken. Once Ken releases Kimeramon, T.K. escapes with the other DigiDestined and the base's prisoners.

Kimeramon defeats the DigiDestined, but Ken can no longer control him. Fearing for Ken, Wormmon leads Davis and Veemon to the power source of the base, the Digi-egg of Miracles. Davis uses the Digi-egg of Miracles to Golden Armor Digivolve Veemon into 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 Kindmess 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.

While searching for Gatomon's tail ring, Yolei, Kari, Ken, and their Digimon enter the Dark Ocean. When they are attacked by Arukenimon's Blossomon, Yolei snaps Kari out of a hysteric state and promises to stand by her. Gatomon and Aquilamon DNA Digivolve into Silphymon and destroys Blossomon, freeing them, despite the tail ring remaining lost.

Having developed a consciousness, BlackWarGreymon comes across Agumon and seeks his advice on his purpose in life. With BlackWarGreymon refusing to obey, Arukenimon creates Knightmon to destroy one of the Digital World's Destiny Stones. Though the DigiDestined attempt to stop Arukenimon, Mummymon, and Knightmon, the damage to the Destiny Stone attracts BlackGreymon and he shatters it.

During a school trip to Kyoto, Yolei encounters BlackWarGreymon and several other Digimon in the Real World after he destroys the second Destiny Stone. Ken briefly returns from the Digital World to bring her Poromon, and their battle attracts the attention of Sora's father, Haruhiko, and Joe's brother Jim.[b] When Musyamon appears, Yolei and Hawkmon defeat and return him to the Digital World.

When BlackWarGreymon destroys the third Destiny Stone, he is convinced that he is destined to fight the Digimon that appears when a Destiny Stone is destroyed. The DigiDestined realize that destroying all the Destiny Stones would upset the balance between all worlds. T.K. becomes frustrated, and despite Angemon digivolving to MagnaAngemon, BlackWarGreymon still destroys the next Destiny Stone.

Cody, worried about T.K., visits Matt, who tells him that T.K. still carries the scars from the battle against Devimon. Determined to stop BlackWarGreymon, Cody personally fronts him. However, BlackWarGreymon is won over by his instincts and destroys the fifth Destiny Stone.

The DigiDestined find Arukenimon and Mummymon at Digitamamon's Chinese restaurant and discover that the final Destiny Stone is hidden in the restaurant's springs. When BlackWarGreymon appears, Angemon and Ankylomon DNA Digivolve into Shakkoumon, preparing to fight with the other Digimon.

As the Digimon fight BlackWarGreymon, the DigiDestined attempt to move the Destiny Stone with their D-3s under Davis' advice. This summons Azulongmon, who had appeared when the Destiny Stones were destroyed. BlackWarGreymon is defeated by Azulongmon and leaves to look for his life's purpose. Azulongmon explains to the DigiDestined about Control Spires and Armor Digivolution, while warning them that Arukenimon is not their true enemy.

On Christmas Eve, the younger DigiDestined hold a party at Ken's apartment while the older DigiDestined attend Matt's concert. Digimon suddenly arrive in the Real World interrupt the concert, forcing the DigiDestined to send them back into the Digital World. The DigiDestined wake up the next day to find that Control Spires and Digimon are appearing worldwide.

As Davis and Ken fight Triceramon in Tamachi, the DigiDestined receive one of Azulongmon's Digicores from a rejuvenated Gennai, which results in not only restoring the original partner Digimons' ability to reach ultimate level, but also allows Paildramon Digivolve into Imperialdramon. The DigiDestined are instructed to meet Gennai's aides and the international DigiDestined worldwide to send the wild Digimon back into the Digital World.

As Davis joins up with Mimi and the American DigiDestined, Kari and Izzy receive help from the Poi Brothers in Hong Kong.

In Australia, Cody and Joe meet with Derek to fight marine Digimon. In Paris, T.K. and Tai receive help from T.K.'s grandfather to save a French DigiDestined held hostage in Versailles by the Mamemon brothers.

Ken and Matt help out a Mexican DigiDestined, while Sora and Yolei helped those in Russia and Siberia. Yolei and Sora are successful in Russia, but they are rescued from an attack by Imperialdramon. The DigiDestined return home in time for Christmas, but while they were traveling, Arukenimon and Mummymon have been gathering children.

The Daemon Corps invade Japan, targeting Ken, and SkullSatamon overwhelms Paildramon. The older DigiDestined Digimon relinquish the power to allow Imperialdramon to transform into Fighter Mode to destroy SkullSatamon. Daemon demands the DigiDestined surrender Ken, but Ken is forced to turn himself into Arukenimon's custody when she reveals the children she and Mummymon abducted.

Ken meets Yukio Oikawa, who knows his past and wants to copy the data of the Dark Spore embedded in his neck for the kidnapped children. The rest of the DigiDestined fight LadyDevimon and MarineDevimon to catch up to him. Yolei and Cody are both forced to watch their Digimon partners kill other Digimon.

With Oikawa's goal complete, he hands Ken over to Daemon. Davis and the other DigiDestined intervene, but Imperialdramon and the other Digimon are powerless against him. As Daemon is able to re-enter the Real World even after being sent back to the Digital World, Ken takes a risk in redirecting the portal to the Dark Ocean. Oikawa lets the kidnapped children return home as he and his followers escape.

While the DigiDestined monitor the children, BlackWarGreymon confronts Oikawa, who tells him the truth about his creation, and tries to attack him. He is stopped by both WarGreymon and Imperialdramon. After a fierce battle, they plead with BlackWarGreymon to befriend them.

One of the children's Dark Spores blooms into a Dark Flower and is harvested by Oikawa, despite the DigiDestined's best efforts to stop him. When Cody's grandfather fails to dissuade him, BlackWarGreymon sacrifices himself to protect him. Noticing that Oikawa is possessed, he uses his remaining power to seal Highton View Terrace's portal to the Digital World.

Oikawa attempts to bring the children to the Digital World, but because BlackWarGreymon had sealed Highton View Terrace's portal, they end up in the Dream World. Oikawa's possession manifests as Myotismon, who Digivolves into MaloMyotismon using the Dark Spores and kills Arukenimon and Mummymon. The DigiDestined become fearful, with the exception of Davis and ExVeemon.

MaloMyotismon tempts the DigiDestined with illusions of their dreams, but Davis, whose dream was that ExVeemon could grow more powerful to defeat him, guides them out. The others follow his example, causing the Digimon to duplicate all Digivolutions. The attacks of all the Digimon send MaloMyotismon into the Digital World, leaving only Imperialdramon, Silphymon and Shakkoumon to face him, as he increases his powers.

Assisted by DigiDestined all over the world and the kidnapped children, the DigiDestined weaken MaloMyotismon with their dreams and Imperialdramon destroys him, ending Myotismon’s reign of terror for good. Oikawa sacrifices himself by using the power of the Dream World dimension to become data and restoring the Digital World. Twenty-five years later, everyone in the Real World has a Digimon partner, and the DigiDestined's children hold the responsibility of protecting the worlds.