Tokyo's electronic systems have gone haywire. Taichi, a primary school aged child is suddenly transported to another world inside the internet, encountering a shape of life called Digimon.
Taichi, Yamato and Koshi fight desperately against the enemy Digimon. The missiles are launched at Tokyo. Furthermore, bullets of light fired by the enemy Digimon hit Greymon and Garurumon directly. Then, an enormous white Digimon appears.
Taichi's group is captured by a Palmon who mistakes them for fruit thieves and brings them to Mimi Tachikawa, the self-proclaimed queen of a village of Tanemon. Ogremon attacks the village.
The group attempts to convince Joe to join them on their quest but he refuses, being more worried about middle school entrance exams than saving the world.
The group are rescued by Yamato and his partner Gabumon, who reveals that there is a Gorimon sniping at them from atop a fortress. Certain that the others will only hinder him, Yamato leaves them behind and goes solo.
With MetalTyrannomon pursuing them, Taichi and Agumon decides to stay behind and distract the enemy while the others make their escape. Koshiro pinpoints the location of the Holy Digimon. A new level of digivolution reached.
Separated from the others, Yamato, Sora and Joe are ambushed at the desert when a Scorpiomon appears and attacks them. Yamato realized that he needs to step up his game to defend his friends.
Mimi and Palmon wander after falling into the ruins, coming across a deactivated Guardromon among piles of robotic Digimon parts whom Mimi express sympathy towards.
Koshiro, becomes distraught as his tablet shuts down at a critical moment. Separated from the others, cornered by Okuwamon, Kabuterimon helps Koshiro to realize his true power.
Yamato's group arrives on a snowy mountain where they stopped for a rest. Joe's determination to protect his friends no matter what triggers a new evolution.
Taichi's group travels through a cave only to find themselves in Tokyo, and notice that despite the previous problems everything seemed suspiciously normal.
Yamato tells Taichi about his younger brother. Meanwhile at the real world, Hikari gets separated from her mother amidst the confusion. The children must fight together to defeat Orochimon and save the real world.
As the countdown runs, a massive surge of energy descends from the real world, reviving Orochimon. Koshiro concludes that Nidhoggmon was the responsible for the blackouts in Tokyo, absorbing the city's energy.
Koshiro informs Taichi and Yamato that he and the other children returned safely to the real world, but their Digimon are missing. The two decide to keep searching for the Holy Digimon when they come across Leomon and co.
Yamato discovers that his younger brother Takeru is in the digital world. A Velgrmon appears and kidnaps Takeru. A new hope breaks free and rushes to his aid.
Taichi and the others chase after SkullKnightmon who stole the holy DigiEgg but they are stopped on their tracks by a Miasma-energized Splashmon. Takeru comes across a trapped massive Digimon called Eldoradimon.
Taichi, Yamato and Takeru fight their way inside Eldoradimon in search for the Digi-Egg. Yamato's willingness to protect his brother helps transform WereGarurumon to a new mode.
By controlling the miasma, Devimon overpowers MetalGreymon and WereGarurumon. Meanwhile at the real world, Koshiro deduces that Calmaramon is sending massive amounts of data to the Digital World and that Taichi's group must be in trouble.
While crossing the sea, Taichi and Greymon are dragged into the water by two sea Digimons. In the Real World, Koshiro must tap into the network to send a signal across the world to stops the ships from colliding.
Taichi and the children wonder how did Hikari come to the Digital World. Just as they are about to reach the continent, A Groundramon appears and starts absorbing energy from the weaker Digimons and attacks the children's Digimons.
Angemon fights DarkKnightmon, who attempts to kidnap Hikari, but the energy generated by their confrontation sends the children away, teleporting each of them with their Digimon to a different place.
Parrotmon appears and joins the fight against MetalGreymon. Taichi and Agumon refuse to give up and continue to fight despite being outnumbered and in a disadvantage.
Lopmon approaches Taichi and Sora, telling them about the ancient war against darkness, and that the dark energy is the fragments of Milenniumon, a powerful evil Digimon they defeated in that war.
Takeru and a weak Patamon are chased by a Fangmon when Taichi and Sora arrive to rescue them. When the fight goes in their disadvantage, Patamon's bond with Takeru gives him the power to evolve again.
Taking Hikari and Moon=Millenniumon with her, SkullKnightmon evolves into DarkKnightmon and begins the ritual to revive Millenniumon. Hikari finally reaches the source of the voice that was always calling for her.
Taichi's group takes shelter in an underwater city led by MarineAngemon. Tailmon insists on fighting alone to protect Hikari from the attack on the city. Hikari convinces her that they must fight together.
Tailmon reveals to Hikari that she feels uneasy with the idea of evolving since she was transformed into SkullKnightmon by Millenniumon's influence. Hikari calms Tailmon down while promising to always be by her side.
Gabumon has been captured by an evil digimon to be dedicated to Millenniumon as a worthy sacrifice. Yamato is willing to rescue his partner with the help of Joe and Gomamon.
The children arrive at a restaurant. Joe makes a new friend, A Potamon that shares the love for eating fries. when Potamon evolves and goes dark, Joe must step up to the leader position he gave himself to save his friend.
When the group rests and spends some time relaxing and playing soccer, a floating island appears in the skies and some bombs start to rain. Sora's memories of playing soccer with Taichi gives her the strength to save her friend.
Yamato and Takeru with their Digimons arrive at an amusement park which reminds the two brothers of going to one when they were younger with their parents, until they realize that there is something not right about the place.
Etemon and Volcamon argue to decide which of the two is best suited for the title of King of Digimon, until they decide whoever defeats the Chosen Ones will be the King.
The Chosen Children end up in a forest where they look for food. Hikari realizes that the forest is alive and it is a huge Digimon called Petaldramon who is having a fight for survival.
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.
Taichi, Yamato, Koushiro, and Takeru are captured by Millenniumon's servant, Sephirotmon, who places them in battle against previously defeated foes. Devimon appears again. He confronts and nearly corrupts Angemon.
Taichi and Agumon along with Nohemon are tasked with rescuing Joe and Gomamon from a pair of Dinosaur-type Digimon that are fighting each other over the only source of water in the area.
The Chosen Children have finally reached FAGA where they are challenged to fight a Mega Machine-type Digimon called Mugendramon, for their full power to be witnessed by Millenniummon.
The Chosen Children and their Digimons are devastated because of the unknown fate of Taichi and WarGreymon. However, clocks are ticking and they need to overcome their sorrows and prevent the resurrection of Millenniumon.
Millenniumon is finally revived. Taichi and Agumon have survived their encounter with Mugendramon. The Chosen Children are trapped. The holy digimons HolyAngemon and Angewomon must fulfill their role in the new war once again.
