Taichi and Agumon act as bait so that the jungle’s Digimon can safely escape. However, Metalgreymon’s attacks are useless against the new Mega Digimon that stands in their way.

Thanks to Koshiro’s group destroying the obelisk which was transferring energy to the Digital World, Taichi and the others defeated Neodevimon at last. However, Taichi struggles against the overwhelming powers of Donedevimon

Taichi and Agumon finally surpassed their limit, and Agumon evolves into Wargreymon. This evolution awakens Lopmon’s long-lost memories. And Taichi learns about the new threat, Millenniumon.

The Digi-Destined come across an old race track. Garurumon is thrilled to challenge Machmon,it's last remaining competitor in a race. The twists and turns of the race with the Yamato-Gabumon's bond enables them to reach the Mega level.

Yamato joins Taichi and Koshiro on their mission to stop the Argomon hacking into the U.S. military. On their way there, they learn the Argomon hijacked an American nuclear submarine which is about to launch a nuclear missle. Greymon and Garurumon work together to defeat the Argomon leader who evolves into a perfect form. Yamato then comes with an idea to defeat the leading Argomon which would endanger Greymon and Garurumon, but Taichi convinces him to proceed as their Digimon launch point blank attacks at the Argomon leader. But the Argomon leader survives and evolves into his ultimate form as the missile is launched. Koshiro informs them that the missile is targeting Tokyo, and when Taichi and Yamato refuse to give up, their Digimon partners suddenly merge into Omnimon when Hikari and Yamato’s younger brother Takeru came in contact with some feathers falling from the sky.

The six children and Digimon neutralize the fortress thanks to excellent teamwork. They try to decode the enemy’s communication log and obtain new information about the Holy Digimon. However, it’s not long before new enemies approach the fortress one after another.

The six Chosen Ones who had finally gathered split up again into two teams in order to find the Holy Digimon. As Yamato’s team attempts to cross the desert, they encounter some dust devils.

Yamato’s team flies above an endless jungle on Birdramon until they come across a floating fortress. Sora’s caring heart that wants to save Digimon in trouble brings about a new glow on Piyomon.

Taichi’s team reaches a canyon where they are attacked by a swarm of insect Digimon. In the chaos that ensues, Koshiro and Tentomon stand up to protect their friends.

Taichi’s team finds a strange cave that leads to Tokyo. Excited to be back, the children attempt to get home through the subway. However, a creepy Digimon prowls the city, and there, the children learn a shocking truth.

Yamato’s younger brother, Takeru, is unexpectedly found in the Digital World, held captive by a powerful Digimon. With the help of Leomon’s army, Taichi and Yamato attempt to save Takeru.

Thanks to Takeru’s bravery, Taichi and the others found the way into the castle where the Digitama is held. As for the Chosen Ones in Tokyo, they were in a remote battle against Calamaramon to stop an uncontrollable tanker from crashing.

Devimon’s castle collapsed after the fierce battle with Darkknightmon and Taichi’s group comes to face Devimon at last. Meanwhile, the rest of the Chosen Ones and their partner Digimon fight to destroy the obelisk that is transferring energy.

Taichi’s younger sister Hikari and Koshiro's group are brought to the Digital World just in time to save Taichi's group. The Chosen Ones are now reunited once again. However, another disaster, this time at a rocket launch site, hits the real world.

The Chosen Ones come to face their old enemy, Darkknightmon. Patamon evolves into Angemon again to fight off Darkknightmon. However, the children are all separated and sent to different parts of the continent.

Hikari is suddenly taken away by Skullknightmon and Taichi could do nothing but watch. On his mission to save Hikari, he meets many kinds of Digimon in the jungle and fights for them as the jungle burns.

Taichi’s party finally catches sight of Skullknightmon and Hikari, who was kidnapped. Taichi chases after them, but Hikari is swallowed into the darkness.

Taichi’s party leaves behind the beautiful underwater city and continues their journey toward the Eternal Continent’s center, FAGA. The party swims through the sea caves on Komondomon, but Digimon with powerful, dark energy block their way.

Taichi’s group reunites with Koshiro and Tentomon after rising to the surface. Koshiro figures out a plan to stop the International Space Station from crashing into Tokyo. Will the Chosen Ones make it in time?!

The Chosen Ones come across an unfamiliar forest. There they meet Etemon and Volcamon who are battling over the title for the King of Digimon. Taichi and others are dragged into their fight.

Takeru and Angemon must face an old enemy...

The time frame for Tokyo's urban functions coming to a halt was drawing near. Taichi, Agumon and Sora head for a "shrine" written about on a lithograph of the Digital World in search of clues. Meanwhile, Koshiro, who is at another location in the Digital World, continues to gather information along with Tentomon, the Digimon he met there, while keeping in contact with Taichi. During that time, Koshiro and Tentomon get swallowed by a mysterious huge Digimon...

Taichi’s party comes across an orchard and meets a mysterious girl, Mimi. Taichi and his friends find out that a kingdom is targeted by some ferocious Digimon.

The children now know that the Holy Digimon is the key to saving Tokyo from the blackouts. They attempt to cross the sea to get to the continent, but they’re suddenly attacked by a mysterious whirlpool.

The battle between Greymon and Orgemon ended abruptly and now the Chosen Ones discuss their next move. Taichi and Agumon take a chance to defeat the ultimate enemy, so that the others can safely head to their next destination.