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.

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.

The kids come across a beach with numerous phone booths, but none of them seem to work.

The kids run away from a Monochromon battle. They come across a trolley car on a small island and decide to spend the night in it, until they are attacked by a Seadramon.

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.

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.

Tai and Agumon land on a snow-covered island and are forced to defeat a Frigimon.

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.

While at camp, Tai, Matt, Sora, Izzy, Mimi, Joe, and T.K. come across seven Digivices and are transported to a strange Digital World where they make friends with creatures called Digimon who claim to be their chosen partners.

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.

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 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.

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.

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.

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.

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 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.

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.

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.

The kids come to a Yokomon village to rest for the evening until a Meramon attacks.

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.

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.