Piximon sacrifices himself trying to save the digidestined from Piedmon. Our heroes find themselves back in the Digiworld, on the shores of MetalSeadramon's ocean domain. Shellmon attacks them, but they defeat him with little difficulty. MetalSeadramon sends his henchman, Scorpiomon. He and his evil master nearly succeed in barbecuing the kids and their Digimon. They're only saved when Togemon and Ikkakumon warp-digivolve into Lillymon and Zudomon. It's a close call, and Tai and the others doubt that the Digimons' abilities have developed enough to defeat their enemies. As if to prove it, Metal Seadramon reappears.
After Whamon and the Digidestined escaped, MetalSeadramon and his henchmen, the Divermon, set out to find them. Izzy discovers that War Greymon has the ability to destroy Dramon type of Digimon, like MetalSeadramon. The Divermon find and attack Whamon, who takes them on a deep pressure chase towards the bottom of the sea. The Divermon can't follow that deeply so the kids escape, temporarily. Using a makeshift SONAR device, Izzy finds a tunnel that leads to safety. However, Metal Seadramon intercepts them before they have a chance to escape. Whamon burrows his way through the tunnel and winds up safely in a bay, near land. But Metal Seadramon follows them through and attacks. Agumon warp digivolves into Wargreymon, who attacks MetalSeadramon.
MetalSeadramon is about to destroy WarGreymon, but Whamon swims in front and takes the deadly blast. WarGreymon then destroys MetalSeadramon with his own River of Power. Tai is excited to fight the other Dark Masters. Puppetmon devises an evil plan to destroy the kids. He makes voodoo dolls of the kids and separates Matt and T.K. from the others. Puppetmon corners T.K. and Kiwimon attacks the other kids. T.K. tricks Puppetmon and smashes his voodoo dolls. The Digimon defeat Kiwimon. Puppetmon swears revenge on T.K. Matt strangely vanishes.
Tai and the others search for Matt, who's mysteriously walked out on the group. Matt is uncertain of his role in the group and is frustrated that the others are getting stronger and more confident. Cherrymon, a sinister and clever tree-like Digimon finds Matt in this vulnerable condition and convinces him that he must defeat Tai if he's ever to fulfill his potential. Meanwhile, Puppetmon and his nasty henchmen, the Garbagemon, attack the others. They have their hands full until Matt and MetalGarurumon suddenly appear and ice the last of their attackers. Then, to the others' amazement, MetalGarurumon turns on Tai's Digimon, Agumon and challenges him to a fight.
Matt and Tai have a heated argument. Matt doesn't understand why the kids were chosen to be DigiDestined and wants to leave. MetalGarurumon and WarGreymon start to fight. Matt and Tai begin to fist fight. Everyone starts to get upset and several Digimon begin to get cross with each other. Puppetmon laughs because this was his plan all along. A friendly entity takes over Kari's body. All the kids and their Digimon are suddenly flying into the sky. Kari (the entity) explains that they are surrounded by computer images from the past. The kids are taken through the past and are shown how they were chosen to be DigiDestined. The crests represent the best quality that each child had four years ago. If that trait is lost, a Digimon can become corrupted. After the story, Kari returns to her body. Matt wants to be alone and leaves. Mimi wants to stay put and not move on with the group. Joe stays with her. The rest go on their way.
Ogremon is being chased by a tribe of Woodmon who are trying to steal his power. A meteor crashes down, scaring the Woodmon away and Ogremon is trapped under a tree. Joe and Mimi rescue him and nurse him back to health. Ogremon is touched by their kindness and becomes their friend. The kids explore Puppetmon's mansion. Puppetmon finds Joe and Mimi and MetalEtemon appears. While Puppetmon and MetalEtemon fight, Tai and the group meet the mansion guards who despise Puppetmon. One of the guards agrees to lead a cannon attack against Puppetmon. Ogremon tells Joe and Mimi that he wants to destroy Leomon. MetalEtemon finds the kids hiding in a tree and chases them through the jungle. A creature that resembles Leomon appears during the chase.
Mimi and Joe encounter SaberLeomon. He takes them to a safe hiding place with Ogremon. They meet up with Otamamon and Gekomon. Puppetmon challenges the other kids and leads them to a crowd of nasty Red Vegiemon, whom they destroy. Puppetmon is angered and makes his house come to life and tries to crush the kids. MetalEtemon confronts Leomon, who digivolves back to SaberLeomon and they fight. Ikkakumon super-digivolves to Zudomon to help destroy MetalEtemon. Puppetmon tries to enlist MetalGarurumon to attack the kids, but he refuses and destroys Puppetmon. A dying Leomon tells Mimi that he will come back to life in the Village of the Beginnings, which has been demolished. Ogremon, Mimi, and Joe vow to defeat the Dark Masters and restore the Village.
As Tai and the others wander the desert, Kari collapses, ill. Tai becomes very upset and the others learn that years ago, Kari almost died because of Tai's negligence. Kabuterimon leads them to a deserted city where Kari can rest, while Tai goes to find medicine for her. With Izzy's Internet skills, they finally track the medicine down, only to find that Izzy's computer has led Machinedramon's evil forces to them. Izzy uses his computer to throw them off track and he and Tai manage to escape. They return to the others-- just in time to see their temporary home obliterated in a missile attack. The others got out in time and a happy reunion is shared by all. Machinedramon appears. The kids run into a building and Machinedramon causes it to crumble on top of them.
The kids have fallen into the sewers beneath Machinedramon's city. Sora, Biyomon, and Patamon find Kari, T.K., and Gatomon, as Kari awakens from her fever. Izzy, Tai, and their Digimon landed somewhere else. As Kari's group searches for Tai's group, they run into WaruMonzaemon, who has enslaved the Numeron. A strange light emerges from Kari, which makes the Digimon stronger than ever. With Kari leading, the group overtakes WaruMonzaemon and frees the Numeron. The group decides to follow the light, hoping it will lead them to Tai and the others. Machinedramon destroys WarMonzaemon. Tai, Izzy, and their Digimon look for Kari's group. They run into Andromon and are attacked by Machinedramon. Soon after, they run into their friends. The strength of Kari's light enables WarGreymon to defeat Machinedramon.
Tai and his crew are confronted with the powerful and ruthless LadyDevimon. Tai divides his forces, sending Sora and T.K. to find the others. Mimi and Joe find Elecmon in the destroyed Village of Beginnings and convince him to join their cause. Suddenly, Joe announces that he and Gomamon are going off for a while to find their place in the world. Meanwhile, with WarGreymon's help, Tai and his crew defeat LadyDevimon. But there is no time for celebration, as they are immediately faced with a far deadlier foe: Piedmon, the last of the Dark Masters.