When Tai and Joe call her a spoiled brat she has them all thrown into a dungeon. Sora finds Matt's boat, but becomes depressed when she doesn't find Matt himself. Both WarGreymon now restored to full strength by the Crest of Friendship and MetalGarurumon prepare to battle Piedmon. Matt and Izzy find their crests. Izzy checks his computer and Gennai tells him that the other kids are asleep in their houses. Matt leaves the group again. MagnaAngemon restores the DigiDestined to their rightful forms as Mimi arrives with the reinforcements.
Matt doesn't understand why the kids were chosen to be DigiDestined and wants to leave. They eventually defeat him with help from Joe's repetitive chanting. When the babies start crying, though, T. Shellmon attacks them, but they defeat him with little difficulty. They are captured by a band of Bakemon intent on eating them. Matt's Digimon gains strength when he realizes that he and Tai are closer friends than ever.
Piedmon attacks again with his army of Vilemon, but Mimi arrives with her army of Digimon, who are able to defeat the evil forces. They then meet Digimons and a friendship developed. Since he's the only kid with a crest, Tai stuffs Agumon with food so he'll have the energy to digivolve to his ultimate form if it's needed. Gennai tells Izzy how to create a Digital Barrier to protect his family from Bakemon. When the Digimon try to digivolve to fight him, Etemon stops them with his rock 'n' roll Concert Crush. He tries one last attack to destroy both worlds, but the power of the Digivices contains the blast.
A ferocious Digimon named Devidramon attacks and Greymon digivolves into Metal Greymon and destroys Devidramon. The Divermon can't follow that deeply so the kids escape, temporarily. They end up in a mysterious mansion which proves to be a hallucination created by Devimon. Puppetmon is also defeated by MetalGarurumon. The kids and their Digimon friends decide to search for whoever built the phone booths. It is revealed that Kari is the eight DigiDestined and that Gatomon is her partner. After saving a plane, they realize that they must hold off on enjoying time with their families, and instead must return to the Digital world to save it once more.
They return to their original forms and are ready to battle Apocalymon. Everyone starts to get upset and several Digimon begin to get cross with each other. Tai goes home and visits his little sister, Kari, who seems to be aware of the DigiWorld. Machinedramon is then defeated by WarGreymon. A friendly entity takes over Kari's body. The kids are saved when Sora's Digivice transforms Leomon back to his good nature, and he detains Ogremon while they escape. WarGreymon then destroys MetalSeadramon with his own River of Power.
Mimi strings them along, never quite awakening the sleeping giant. The kids continue to search for the child before Myostismon can find him or her. DemiDevimon attempts to buy Izzy's crest from Vademon, and in the confusion, Izzy recovers his crest and his curiosity. However, the Digital world seems to appear in the Sky, and anything that touches it or the Digimon that seem to come out of it, freezes. They meet up with Otamamon and Gekomon. The kids and their Digimon sail a raft to Server, but they're swallowed by Whamon en route.
They remove a Black Gear from Whamon's stomach, and in return he takes them to where Devimon hid the tags. Izzy manages to reveal the order of the cards, but is left out with two more cards for one space. Datamon tries to drop Etemon into a black pit, but he, the pyramid, and Etemon's forces are dragged in, too. The humans soon figured out that Digimons are in fact, not bad, the situation made them bad. Matt's crest glows and Garurumon Digivolves to WereGarurumon and defeats Digitamamon.
Then, to the others' amazement, MetalGarurumon turns on Tai's Digimon, Agumon and challenges him to a fight. Miharashi, a volcano guarded by the flaming Meramon. Tai gets the Digivice back to Kari, which helps Gatomon Digivolve to Angewomon. Joe doesn't know that DemiDevimon has ordered Vegiemon to keep Joe working there forever! However, Gennai informs them that although the timeline has been restored, there is only a small window of opportunity to leave and the children either have to leave now or remain in the Digital World forever. But this only works temporarily and, with the arrival of the towering Dark Tyrannomon, things look bleak until Togemon transforms into Lillymon, and tames the beast. At the last second, Izzy cracks the code of the cards and the kids leap through the gate! Duane accidentally knocks Izzy off a bridge during a confrontation and Motimon digivolves into Tentomon and saves him. Gomamon and Biyomon digivolve to Ikkakumon and Birdramon to fight the Bakemon, and with the help of some quick thinking by Joe, they defeat him.
Phantomon follows Sora to Matt and Kari's hideout where he summons two Digimon to destroy the children. When Myotismon tries to attack, Wizardmon saves Kari and Gatomon, but at the cost of his own life. Fleeing, they come across Izzy and Tentomon. He also discovers that evil Digimon are taking advantage of the rift and creating chaos on Earth. The transmission cuts out before Gennai can reveal the identity of the evil force. Birdramon and Togemon fight him off, freeing the boys and their Digimon, and everyone flees, but Cockatrimon chases them in his ship.
As they enter, they fall into the trap of one of Metalseadramon's minions,. The kids' faith in themselves restores the power of their crests. . Puppetmon laughs because this was his plan all along. They eventually escape and defeat Scorpiomon, who is then destroyed by Metalseadramon. Izzy and Tentomon go after Raremon.