Fourteen-year-old street fighter Marcus meets a strange dinosaur-like creature. This strange creature, "Agumon", is a "Digital Monster" from the "Digital World".

Marcus tries to hide Agumon from DATS in his house, but DATS quickly concludes that he is there, so they send Yoshi to investigate.

A new member of DATS appears from Austria: Thomas H. Norstein, a fourteen-year-old genius who looks down on Marcus. Because of their different behavior, the two start to fight over everything.

Marcus and Thomas are ordered to work together, but they aren't able to do so, which becomes clear during the pursuit of a group of Numemon. Suddenly a Drimogemon appears and helps two burglars steal money.

Marcus and Thomas, together with their Digimon partners, enter the Digital World to capture Drimogemon.

Although Agumon and Marcus work well together to defeat a Tortomon, Agumon gets angry at Marcus after a comment of his and now hides in his Digivice.

It's Kristy's birthday and Marcus must attend supplementary exams to save his grades. Unable to be by his sister's side on this day, he asks Thomas to take his place. A Citramon, however, threatens to ruin everything.

Yoshi is dating a famous musician, Neon Hanamura, who is also her childhood friend.

A famous boxer has a fantastic comeback after being absent for some years because of an injury. Thomas is a great fan of his, and when rumors of him using a Digimon to help him in his fights start to spread, he investigates, determined to prove his innocence.

Thomas invites Kristy, Marcus, and Agumon to his mansion for lunch. Marcus becomes the unfortunate victim of strange unexplained accidents.

The owner of a store that specializes in baking white buns suddenly becomes addicted to gambling. For unknown reasons, he has consecutive winning streaks in every bet, all thanks to the prayers he has paid to a mysterious shrine.

Kristy's made a new friend, a Digimon called Biyomon. Although Marcus feels optimistic for his sister and consents to let Biyomon stay, he's later told that people can't keep a Digimon they've made a relationship with if they aren't DATS members!

Merukimon appears in the real world to prevent Falcomon from being defeated, defeating easily the DATS Digimon and reverting Biyomon to a Digi-egg in the process. In a desperate attempt to find his way back to Kristy after Merukimon revives him, Biyomon loses control and quickly evolves to Aquilamon and then into Garudamon, wreaking chaos over the city.

To stop Merukimon's further assaults on the human world, DATS authorizes Yoshi, Thomas, and Marcus to be dispatched into the Digital World.

As they wander further into the Digital World, the DATS stumble upon a ghost city which is home to a nest of Dokugumon. Without warning, the spider Digimon quickly trap the DATS and their partner Digimon, dragging them all into the depths below where their lord MetalPhantomon dwells.

Yoshi's struck by a contagious virus which seemingly affects humans, though Digimon remain immune to its effects. With Marcus and Thomas gone for supplies and Lalamon alone nursing Yoshi, Keenan and Falcomon take advantage of the opportunity to get rid of the crippled Saver, only for the boy to become infected as well.

Yoshi has lost her battle confidence, feeling like she's always dragging down her companions. The group is caught up in an avalanche caused by Mammothmon, and Yoshi, Thomas, and Lalamon fall down to the bottom of a valley.

After overcoming difficult hardships along their trek, the DATS finally arrive at Infinity Ice Ridge. To their surprise, the old man, Homer Yushima, is waiting for them near the entrance, leading them to a cave shortcut.

With Yushima's help, Marcus, Keenan, and the others are able to return to the real world. However, they are forced to leave Yushima behind in the Digital World.

The DATS arrive at Dr. Crier's home, but Keenan runs away in shock and denial at the sight of his human mother.

Enraged that Merukimon has not taken proactive action to deal with the human problem, SaberLeomon dispatches a Digimon armada consisting of hundreds of Pteramon and Boarmon, led by Gotsumon, to the human world to destroy it.

The Digimon invasion was temporarily halted due to the efforts of a single man, who Sampson knows and who gained the approval of Chief Hashiba. Understanding that Keenan has no place to go, Marcus invites him and Falcomon to stay at his home.

Due to the widespread destruction that the Digimon caused in the city, DATS, acting on orders from the government ministry, dispatches the DATS, along with a troop unit, into the Digital World to defeat Merukimon once and for all.

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The gang appears in the Digital World and head towards Cherrymon's forest for an information gathering.

After their Digivice iC broke, Marcus, Thomas, and Yoshi stumble onto a gym where BanchoLeomon trains them. Can they master their ultimate DNA Charge?

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Both the DATS and the inhabitants of the Holy Capital are preparing for the impending battle. When news arrive that Kurata's camp has been discovered, Marcus takes the initiative to strike a head on assault, but Thomas disagrees since it may be a trap. However, Thomas feels underappreciated witnessing how all the Digimon support Marcus.

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Kurata unleashes Belphemon on the city, causing Yoshi, Keenan, Miki, and Megumi to confront him.

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Craniummon is briefed by Yggdrasil about all the events that occurred up to now while Marcus and the others protect the citizens from the onslaught of lightning from the Digital World.

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In order to learn Spencer's true intentions, Marcus and ShineGreymon head once again to the Digital World. However, Thomas and the others stay in the human world to fend off the Royal Knights' ongoing attack with Crusadermon this time directing the assault.

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The DATS team climb Yggdrasil's headquarters, confronting odd crystals that repel their attacks. Leaving the others behind, Marcus, Agumon, and Gotsumon confront Yggdrasil. Meanwhile, Craniummon heads to the real world and confronts Garudamon.

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