The Digimon invasion was temporarily halted due to the efforts of a single man, Kurata, 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. Meanwhile, SaberLeomon himself realises in the human world and rampages at an oil refinery as a challenge to the DATS.

A fourteen-year-old youth named Marcus Damon, who desires to be the best fighter in the world, meets a strange dinosaur-like creature and engages the creature in a fist fight that ends in a draw. At that time, after introducing himself, Agumon vows to be Marcus's follower as the two are confronted by Yoshino Fujieda, a teenaged member of a government agency known as DATS dispatched to capture Agumon. After escaping and hiding Agumon in Tokyo Tower, Marcus is found by Yoshino who brings him to her superior Commander Sampson. Commander Sampson and his Digimon Kudamon explain to Marcus that Agumon is a wild creature that will go out of control. Though Marcus dismisses this with the intent to bear any responsibility for anything Agumon does wrong, an alarm of a burger joint being attacked is reported in the area Agumon was hidden in. Though it appeared Agumon was the cause, it turned out to be the work of a Kokatorimon. After Kokatorimon knocks Agumon out, a furious Marcus sprints towards Kokatorimon and punches the bird in the face. Astonished of the energy generated from his fist, Marcus encounters a mysterious old fisherman who gives him a Digivice to channel his charged DNA in so Agumon can become stronger. This causes Agumon to Digivolve into GeoGreymon, defeating Kokatorimon as it reverts him into a DigiEgg. Commander Sampson is impressed by the turn of events.

Brought to DATS HQ by Yoshino, Marcus and Agumon learn that wild Digimon are placed in a teleporter to be sent back to the Digital World. With DATS still seeing Agumon as a threat, Marcus stops them from forcing Agumon into the teleporter and the two escape. Marcus resolves to hide Agumon at his house, only for the Digimon's existence to be found out by his mother Serah Damon and his younger sister Kristy Damon. From there, to Marcus's annoyance, his family and Agumon all quickly become friends. Marcus is further annoyed when he learns that Yoshino is going to keep an eye on him and Agumon indefinitely unless the youth becomes a member of DATS. The next day, Marcus passes by Kristy's school and learns that something is attacking the school's animals. Marcus plans a stakeout of the cages and places Agumon inside as bait, the culprit revealed to be a Kunemon that has been feeding off the emotions of Kristy's young classmate Takashi who secretly wished the animals would just disappear. No longer needing Takashi, Kunemon attacks with Yoshino's Digimon partner Lalamon digivolving to Sunflowmon to fight the wild Digimon. However, Kunemon digivolves to Flymon and uses his poison powder to paralyze Sunflowmon and Yoshino. By that time, have been unable to digivolve Agumon, Marcus learns how to access his DNA and activates it by punching Flymon before it is defeated by GeoGreymon. The old man who gave Marcus his Digivice then appears, telling the youth of the Digital World and all the opponents he could fight there. Returning to DATS HQ, Marcus is welcomed by Commander Sampson as a new member of DATS.

At the Damon household, everyone is preparing themselves for the day ahead when Marcus receives a call from DATS that a DemiMeramon has begun attacking some men who. However, due to DemiMeramon's lack of body mass, neither Agumon nor Marcus could do any damage which makes the latter unable to activate his DNA. As the two run off after DemiMeramon after he flew off, a blond-haired youth arrives and wipes men's memories of the attack before going after the wild Digimon. A while later, unable to find DemiMeramon, Marcus learns the wild Digimon was captured by the blond-haired youth who is identified as the child genius Thomas H. Norstein who has returned after six months of being at DATS's Austria branch. Because of their different personalities, Marcus and Thomas get on each other's bad side as they end up having a boxing match before learning that DemiMeramon spawned from original's flame sparks are attacking the city. Sent by Commander Sampson to battle the DemiMeramon, Thomas has his partner Gaomon digivolve into Gaogamon to defeat them. However, three DemiMeramon remain at a chemical plant close to DATS. Starting to suffer self doubt after seeing Thomas and Gaomon fight, Marcus runs off before finds the old fisherman cooking a fish on a makeshift stove, the man's speech of fanning flames giving Marcus an idea. Confronting the DemiMeranon, Marcus has Agumon use his fire to strengthen them until they combined and digivolve into Meramon. Marcus, now having an opposite he can hit, is then able to punch Meramon and has GeoGreymon finish the wild Digimon off. Later, to both their dismay, Marcus learns that he and Thomas are to be teamed up.

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 try to capture him, but because of their quarreling, he escapes to the Digital World. To capture him, Thomas decides to follow him, even against the orders of Commander Sampson.

Marcus and Thomas, together with their Digimon partners, enter the Digital World to capture Drimogemon. They fall into a large underground labyrinth, Drimogemon's home, and escape seems impossible. Thanks to Marcus' unconventional methods, they manage to leave the labyrinth on Drimogemon's back, but then, the wild Digimon evolves to Digmon.

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. Meanwhile, an Elecmon wreaks havoc in the city, causing car crashes. Marcus tries to defeat him alone, but Elecmon Digivolves to a black Garurumon, which even Sunflowmon and Gaogamon can't defeat. Marcus and Agumon must work together again to beat this new threat.

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. The real reason for her to approach him is because he is suspected of hiding a Keramon (who later digivolves into Kurisarimon), using him to bolster his career.

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. Agumon sees the culprit is a Soulmon, who is invisible to everybody else except for him. Marcus and the others do not pay attention to Agumon's warnings, and the pranks become more frequent and more dangerous.

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. As the man sinks in his obsession for gambling, he neglects both his business and his own son. Touched by the boy's relationship with his father, Marcus sets out to speak reason to the man, but he can't imagine that the wrongdoings of Vilemon and his DemiDevimon henchmen are at work.

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. The DATS and their Digimon feel helpless before the overwhelming power of the Ultimate Digimon. Frustrated at not being strong enough to protect the smiling faces of both his family and friends, Marcus lets out a cry that awakens the birth of a new DNA Charge that allows GeoGreymon to digivolve into his Ultimate form, RizeGreymon.

To stop Merukimon's further assaults on the human world, DATS authorizes Yoshi, Thomas, and Marcus to be dispatched into the Digital World. Unfortunately, their presence does not go unnoticed by Merukimon and a mysterious shadow, who quickly ambushes the DATS after their arrival. The attacker turns out to be a ten-year-old boy named Keenan, who harbors an intense hatred for humans.

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. He casts the DATS into a world of endless nightmares and despair where their greatest fears take shape. After reliving a painful memory about his mother, Thomas' DNA awakens, granting Gaomon the power to digivolve into his Ultimate form, MachGaogamon.

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. Worried for the sake of Keenan, Falcomon strikes a deal with the other DATS to lead them to the whereabouts of a vaccine that lies in Wanderer's Cape that can counter the effects of the virus. Meanwhile, Gotsumon sends Blossomon to prevent the vaccine from being obtained.

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. To protect Yoshi and the wounded Thomas, Lalamon faces off against Mammothmon, not losing her fighting spirit. Yoshi swirls in despair until Lalamon sings a song to tame the beast that triggers an old memory from Yoshi's childhood of the time she and Lalamon met. Having restored faith in herself, Yoshi calls out her own DNA Charge to digivolve Lalamon to Lilamon.

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. Once inside, they make their way through a swarm of Tsumemon, and then against Keenan, who is bound to defeat the humans once and for all. However, Gotsumon betrays Keenan and takes the whole group hostage, except for Marcus, delivering them all before Merukimon. Saving Keenan from certain death, Marcus and Agumon hurry to Merukimon's palace for a final showdown.

Yushima's true identity as the commander of the Digital World exploration party, as well as the DATS chief, is revealed. 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. Marcus makes a big uproar, trying to do all it takes to go save him, but the Digital Dive is frozen over. Sampson tells Marcus and Keenan about the incident that occurred ten years ago. To make matters worse, MeruKimon's Gotsumon appears in the real world with three Okuwamon to target Keenan.

The DATS arrive at Dr. Crier's home, but Keenan runs away in shock and denial at the sight of his human mother. Drowned in his sorrowful thoughts, Keenan recalls his memories of Frigimon's death, which bring him grief. At the Crier's home, the Professor explains that his wife, Michelle, went into shock and a partially catatonic state after the search for Keenan in the Digital World confirmed his disappearance. Suddenly, an anomalous thunderstorm strikes the house, causing the digital gate to open up, and Hagurumon comes from it. It immediately takes over the house and transforms it into a bizarre, toy-robot-like creature with Michelle trapped inside.

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 DATS step in to contain the threat but are overwhelmed in numbers by the enemy, until the rest of the DATS staff enters the battlefield to help them in the fight. However, both sides are unaware that an unseen third party, lurking in the shadows, has had them all set up in a trap.

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. Thomas' suspicions about Kurata grow stronger when it is made known that the latter has been appointed leader of the mission. Meanwhile, Keenan still cannot gather himself to reconcile his Digimon feelings with his human identity, until Sarah's kind words encourage him and build his resolve to go into the Digital World and stop the war between Merukimon and DATS.

Ten years ago, Frigimon found an abandoned human baby, Keenan, and took him as her son. An expedition led by Professor Spencer Damon embarked into the Digital World to search for the lost baby but found itself threatened by wild Digimon. After a brief feud, Merukimon realized that Spencer was a honest man and they made a promise that both races would cooperate with each other in the future. However, Kurata became consumed with hatred for Digimon, deeming them all evil due to the attack. Merukimon recalls and denounces him as the man responsible for the deaths of Frigimon and many other Digimon.

Kurata's true ambition is the total annihilation of the Digimon race, making it come about with the aid of his artificially made puppet Digimon Gizumon AT. The DATS and their Digimon partners fight back to no avail; however, Marcus refuses to give up. Fed up with Marcus' stubbornness, Kurata evolves Gizumon into its Ultimate form, Gizumon XT, to finish the DATS. As a dying act of courage, Merukimon sacrifices himself to teach Keenan that a world where humans' and Digimons' hearts become one is possible. Taking Merukimon's words and the happy memories spent with Marcus and the others to heart, Keenan's DNA explodes, allowing Falcomon to access his Ultimate digivolution, Yatagaramon.