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.

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

The kids stumble upon a factory where they find an Andromon in trouble.

While escaping the Numemon who attacked the group in the sewers on their way out of the factory, the kids are split up and Mimi ends up in Toy Town.

Tai and Matt argue whether they should climb Infinity Mountain. Joe and Gomamon decide to climb the mountain by themselves. While on the mountain, they are attacked by a Unimon.

The kids meet the ruler of File Island, Devimon, the controller of the Black Gears.

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

Mimi and Palmon escape Sukamon and Chuumon and cross over to the next island where Izzy and Tentomon landed, but end up getting lost in a labyrinth and attacked by Centarumon.

After an encounter with Ogremon at sea, Joe and Gomamon find themselves on an island with Sora and Biyomon before they are captured by a cult of Bakemon intent on eating them. Gomamon and Biyomon manage to escape and Digivolve to fight Lord Bakemon. Joe uses a Buddhist mantra to weaken Lord Bakemon. After Birdramon and Ikkakumon destroy Lord Bakemon, they ride across the sea to find their friends.

T.K. and Patamon arrive in Primary Village, the place where all Digimon are born. When the baby Digimon start to cry, T.K. and Patamon are confronted by Primary Village's caretaker, Elecmon, which they settle with a tug-o-war match. Patamon wins and earns Elecmon's respect and trust, as he allows the both of them to stay. Meanwhile, Devimon sends Leomon after T.K, considering him a threat.

T.K. is attacked in Primary Village by Leomon and Ogremon, until Tai, Matt, Izzy, Mimi, and their Digimon arrive to his rescue, where they use their Digivices to free Leomon from the Black Gears. Leomon later explains the prophecy that the children, as "DigiDestined", are to the saviors of the Digital World. The group fights Devimon, who absorbs Black Gears and Ogremon. Devimon defeats the DigiDestined, even when Joe and Sora rejoin them. Patamon Digivolves into Angemon when T.K. is in danger and sacrifices himself to defeat Devimon. Angemon's data reconstitutes into a DigiEgg, and File Island begins to reform itself. The DigiDestined are then suddenly contacted by Gennai.

Gennai urges the group to travel to Server in order to defeat another enemy, informing them about Crests, which will allow their Digimon to Digivolve even further. While traveling on the ocean, the DigiDestined are swallowed up by Whamon, who is under the control of a Black Gear. Tai frees him with his Digivice, and as gratitude, Whamon takes the DigiDestined into an undersea store where the Crest tags are located. They fall under attack to Drimogimon and free him from a Black Gear. After recovering the tags, Whamon proceeds to take them to Server.

On Server, the DigiDestined arrive at a Koromon village, only to find Pagumon living there. Despite the Pagumon's warm welcome, they are allied with Etemon and abduct Tokomon at night, imprisoning him with the Koromon. The DigiDestined rescue them, but Etemon uses his Dark Network to defeat them and destroy the village. The group take refuge in a cave, where Tai finds the Crest of Courage, allowing them to escape from Etemon into the desert.

Joe's tag leads the DigiDestined to a coliseum, where Etemon traps them and forces Greymon to fight another Greymon. After Joe finds the Crest of Reliability, the group escapes and Tai forces Greymon to Digivolve to his ultimate form by putting himself in harm's way. Instead, Greymon Dark Digivolves into SkullGreymon, attacking everyone before eventually reverting to a regretful Koromon.

After getting lost in the desert, the group is taken aboard a ship traveling in the desert, headed by Kokatorimon. Kokatorimon captures all the boys and petrifies their partners. Biyomon and Palmon Digivolve and defeat him, and his ship crashes into a giant cactus. Mimi finds the Crest of Sincerity on top of the cactus.

When the group is attacked, Tai and Agumon are hesitant to fight since Digivolving into SkullGreymon. Piximon rescues and trains the DigiDestined at his facility, where Tai and Agumon are stranded in a cave as the others do manual labor. At night, Matt and Izzy sneak away to find the Crest of Friendship and the Crest of Knowledge. However, they are detected by the Dark Network as Etemon sends a Tyrannomon after them. Tai and Agumon regain the courage to fight, leaving to Agumon Digivolve into Greymon and defeating Tyrannomon.

After T.K. finds the Crest of Hope, Izzy receives an e-mail from Datamon, who asks them to rescue him from Etemon's pyramid in exchange for Sora's Crest. Tai, Sora, Izzy, and Joe infiltrate the pyramid, with Tai being overconfident that the Digital World is a virtual reality. However, once Datamon is freed, he kidnaps Sora and Biyomon. Tai becomes too frightened to pursue Datamon after Izzy warns him that they could die.

While the rest of the DigiDestined distract Etemon's forces, Tai and Izzy infiltrate the pyramid to save Sora, where Datamon plans on cloning her to use her Crest and Biyomon to enact revenge on Etemon. Tai musters his courage and saves Sora while Datamon activates the Dark Network to absorb data, including Etemon. Etemon, fused with the Dark Network, fights the DigiDestined, but Tai's Crest allows Greymon to Digivolve into MetalGreymon. When Etemon is defeated, a portal swallows him while Tai and Koromon are sent to Tokyo.

Tai and Koromon arrive home, where they meet Tai's younger sister, Kari, and also learn that not much time has passed since they were in the Digital World. Later, Tai gets a message from Izzy telling him not to return, and he discovers that Digimon are appearing in the Real World. He concludes that they must return to the Digital World and help their friends. After Koromon Digivolves to Agumon to battle an Ogremon, a portal opens and transports both of them back to the Digital World.

Tai and Agumon return to the Digital World to find Tokomon, who reveals that everyone has split up to find them after weeks since their disappearance. Meanwhile, DemiDevimon causes a rift between T.K. and Tokomon and secretly plans on feeding T.K. amnesic mushrooms. Agumon exposes DemiDevimon, and Tokomon Digivolves into Patamon to drive DemiDevimon away.

Matt finds Joe working at Digitamamon's diner to pay off his debt and agrees to help. DemiDevimon bribes Digitamamon to keep them while setting off accidents that makes Matt question Joe. However, once Digitamamon's scheme is exposed, they battle him with Tai and T.K. Joe sacrifices himself to save T.K., leading Matt to see him as a true friend and allowing Garurumon to Digivolve into WereGarurumon. After Digitamamon's defeat, the group splits up and continue their search for the remaining DigiDestined.

Izzy falls into Vademon's pocket dimension and is forced to give up his curiosity. Tentomon snaps Izzy out of his trance, but by that time, DemiDevimon tries to buy Izzy's Crest from Vademon. In the confusion, Izzy recovers his Crest and his curiosity as he causes Kabuterimon to Digivolve into MegaKabuterimon, defeating Vademon. Izzy and Motimon are found by Matt and T.K. soon after.

Tai and Joe find Mimi with the Gekomon and Otamamon, who treat her like a princess hoping that her singing voice will awaken ShogunGekomon. However, Mimi becomes too consumed in being pampered to give it up and imprisons Tai and the others after they attempt to record her voice. After a nightmare, Mimi apologizes and awakens ShogunGekomon. ShogunGekomon, however, attacks Mimi, causing MetalGreymon to defeat him.

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.

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.