With the help of the entire team and their Digivices, WarGreymon and MetalGarurumon are able to defeat VenomMyotismon. However, immediately following the battle they must leave for the Digital World, which is once again in danger.
The kids meet the ruler of File Island, Devimon, the controller of the Black Gears. He, Ogremon and a possessed Leomon, attack the kids who manage to escape, but Devimon breaks File Island into multiple, smaller islands.
Tensions run high as a fight breaks out between Matt and Tai as well as their respective Digimon partners. Kari's body is taken over suddenly by a strange entity, to explain why the children were chosen.
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 attack from Ogremon at sea, Joe and Gomamon find themselves on an island with Sora and Biyomon. They are captured by a band of Bakemon intent on eating them.
Whamon is killed trying to help WarGreymon, who finally manages to defeat MetalSeadramon. The kids then go into a forest were they are continually taunted by Puppetmon, who uses toys to move them around.
Just as the kids are about to be destroyed by MetalSeadramon, Whamon comes to their rescue and they flee to the bottom of the ocean. However, when MetalSedramon catches up to them, a battle begins.
Kari falls ill, and Tai becomes nearly hysterical in his attempts to help her. Machinedramon attacks them in a mechanical city under his control, and the group is separated.
The DigiDestined have a series of misadventures trying to get back to their homes in Odaiba. Eventually, they end up getting a ride from Sora's cousin, Duane.
Kari recovers, and, along with Sora and T.K., begins searching for the others. They run into WaruMonzaemon, and Kari frees the Numemon he has enslaved, who then begin calling her "Queen".
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 after being attacked by a Monzaemon.
Joe and Tai find Mimi being treated like a princess at a palace. Sora convinces her to sing and awaken ShogunGekomon, but ShogunGekomon attacks the kids.
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.
As the DigiDestined return to the Digital World, they learn of the four Dark Masters who have taken it over. MetalSeadramon, Puppetmon, Machinedramon, and Piedmon are all mega level Digimon, and are more than a match for the DigiDestined.