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 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.

When the DigiDestined find the Digi-egg of Friendship, they are attacked by Flymon and MetalGreymon. Davis is conflicted about fighting Agumon at first, but once he realizes he needs to protect his friends, the Digi-egg of Friendship activates and allows Veemon to Armor Digivolve into Raidramon.

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.

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.