Tai and Agumon return to the Digital World to find Tokomon. Tokomon relays what has happened in the time that they have been gone (which is several weeks in DigiWorld time). He reveals that the entire group has separated and that DemiDevimon has tricked T.K. into becoming his "friend." T.K. realizes DemiDevimon's trickery after Agumon exposes him for a fraud. Tokomon digivolves into Patamon and drives DemiDevimon away.

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.

Tai manages to rescue Sora. Datamon pulls himself, Etemon, and many of Etemon's minions directly into the Dark Network. When Etemon reappears, having fused with the network, Greymon digivolves into MetalGreymon to fight him. The battle ends up opening a portal that sucks away Etemon and transports both Tai and Agumon back to Tokyo.

Ken runs away from home, preferring to remain in the Digital World instead. He captures Agumon, and forces him to dark digivolve, resulting in the uncontrollable SkullGreymon.

The group is attacked by a Kuwagamon and Tai fails to digivolve Agumon. Piximon intervenes and saves them. He then offers the group training at his facility, and leads Agumon and Tai into a cave while the others stay outside. When Matt finds his Crest of Friendship and Izzy finds his Crest of Knowledge, they are spotted and attacked by Tyrannomon. Tai and Agumon reappear just in time to defeat Tyrannomon.

Davis' soccer team is playing against genius Ken Ichijouji's team. The DigiDestined later find out that he actually is the Digimon Emperor.

While traveling in the desert, Joe's Tag reacts, leading the group into a Roman-like coliseum. There, they are trapped by Etemon, and Greymon is forced to fight another Greymon. After Joe finds his Crest of Reliability, the group escapes. Tai attempts to force Greymon to digivolve. Greymon digivolves into SkullGreymon and loses control of himself—attacking the others who are unable to stop him. SkullGreymon eventually reverts back to Koromon and apologizes for his behavior.

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.

A mysterious person named Gennai appears as a hologram after a fight with Devimon and urges the group to travel to the continent of Server in order to defeat another enemy. Gennai also tells them about objects called Crests that will allow their Digimon to digivolve even further. They build a raft and leave File Island, but are soon swallowed up by Whamon who is still under the control of a Black Gear. After the gear is removed, Whamon takes the kids to where their Tags—the objects that the Crests are stored in—are hidden.

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.

T.K. and Patamon end up in Primary Village, the place where all Digimon are born. There they are confronted by Elecmon, the guardian of the baby Digimon. He struggles with Patamon, having mistaken the two for intruders. To avoid a fight, T.K. proposes that they settle their dispute with a tug-o-war. Patamon wins and earns Elecmon's respect and trust.

Gomamon is injured and left for dead by the Digimon Emperor. Joe goes with the new DigiDestined to save him. But soon after they come into the digital world, Cody gets hurt, and Joe stays to help him.

Mimi and Palmon are harassed by Sukamon and Chuumon. After escaping them, they cross over to the next island, where Izzy and Tentomon landed. After they reunite, Mimi and Tentomon get lost in a labyrinth and are attacked by Centarumon. Izzy and Palmon finally find them and their Digimon battle and destroy Centarumon's Black Gear. After the battle, Leomon appears and attacks the children, but is driven back by the light of their Digivices.

Gabumon is captured after causing an uprising in a Gazimon village. He escapes and gets badly beaten up. Matt and the rest of the new DigiDestined go to the digital world to save him.

The kids meet the ruler of File Island, Devimon, the controller of the Black Gears. He, along with Ogremon and a possessed Leomon, attack the kids who manage to escape. They end up in a mysterious mansion, which proves to be a hallucination created by Devimon. Devimon breaks File Island into multiple, smaller islands and separates the kids onto the different islands.

The true DarknessBagramon has completely frozen the human world. In the middle of it all, Taiki is reunited with Examon, WarGreymon, and the Digimon who led him to the Digital World, Omegamon. With the help of all 15 of the knights in their order, he formulates a plan, but carrying it out would throw him into extreme danger alone. Can Taiki defeat DarknessBagramon and save the future of his own world?!