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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The DATS team returns to the real world, only to find that Sampson and the others are missing. Chief Hashiba surrounds them and dismisses them from DATS, since Kurata lied to the government, and the memories of Marcus, Thomas, and Yoshi are erased. The Digimon are held captive in a jail cell

With DATS HQ destroyed and Kurata on his way to the Digital World, the DATS seek out Dr. Crier to ask him to reactivate his digital gate. When they go through, they end up running into Kurata's henchmen: Kouki, Nanami, and Ivan

The gang appears in the Digital World and head towards Cherrymon's forest for an information gathering. However, a swarm of Gizumon XT appears where Kurata gains the upper hand and the DATS members are saved by BanchoLeomon. He tells the group to "Search for power" and disappears

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

The DATS arrive at the Holy Capital, but once inside are quickly captured and placed in an arena for execution. There, they meet once again with an old acquaintance who they thought missing. Thankfully, the moment that Marcus displays his DNA, the Digimon set them free, as they realize Marcus is Spencer Damon's son who all remember him for his heroic deeds to them

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

Nanami accomplished to drain all the water in the lake, where ElDoradimon rests, drained thus preventing any means of mobility to the Holy Capital. With the fortress's defenses down, Ivan directs a frontal assault but is soon detained by Yoshi and Rosemon. However, the two of them are in for a surprise when they witness that Ivan has gained a power boost

By incapacitating ElDoradimons' movements, Kurata opened up a massive digital gate that sucks the titanic Digimon along with all its inhabitants to realise into the human world. Once more in the human world, Kouki challenges both Marcus and Agumon for a final showdown to determine the stronger fighter between both. Meanwhile, the other DATS and the digimon citizens are busy fending off the Holy Capital from the intruding Gizumon

ElDoradimon was annihilated by Kurata's Gizlance, and to complicate matters more, Thomas and Gaomon have mysteriously vanished. In fact, Thomas returned to his estranged father and sister, Relena, but the welcome is cold when Thomas' father presents his benefactor none other than Kurata. In exchange for treating Relena's illness, Kurata persuades Thomas to seal an agreement

Because Thomas has pledged allegiance to Kurata, Marcus' fueled with a feeling of deep hatred in his heart to destroy his opponent at any cost that causes him to invoke a Dark-DNA Charge triggering on ShineGreymon to digivolve into Ruin Mode. Fortunately, Kristy arrives to stop Marcus, and he sees the error of his ways but is too late to stop ShineGreymon's rampage. Feeling hopeless, Marcus sheds tears streaming onto his digivice causing ShineGreymon to come into its senses and revert back to digi-egg

Kurata unleashes Belphemon on the city, causing Yoshi, Keenan, Miki, and Megumi to confront him. Thomas double-crosses Kurata, forcing him to become a pure DNA, and fires himself at Belphemon, who in turn transforms into Rage Mode. As Marcus races off with Agumon's digi-egg in hand, can he make it time to assist the others?

In an attempt to defeat Belphemon, Keenan's DNA Charge allows Falcomon to digivolve into Ravemon. Unfortunately, it isn't enough to stop the rampaging Demon Lord. Will Agumon hatch from his digi-egg in time to assist the others and defeat Belphemon once and for all?

To everyone's shock Kurata is well alive within Belphemon and has the demon lord to absorb all the electricity of the city to open a space rift. Thomas alerts everyone that Kurata intends to blow up both human and digital worlds. Everything seems hopeless for the DATS, but Marcus' words rekindle their spirits, that regardless of being human or Digimon everybody present is the DATS team who fight to protect their loved ones

Craniummon is briefed by Yggdrasil about all the events that occurred up to now while Marcus and the others protect the citzens from the onslaught of lightning from the Digital World. In addition, BanchoLeomon makes the ultimate sacrifice

As Marcus and the others make their way to the Digital World, they end up crashing into a shoreline. To their surprise, they find Gotsumon there, reborn and without his old memories. Gotsumon agrees to lead them to Yggdrasil, but along the way, they are attacked by Craniummon

The DATS team arrive back in the human world, thanks to Sleipmon, who is none other than Commander Sampson's Kudamon. Gallantmon attacks the human world and makes short work of MirageGaogamon, Rosemon, Ravemon, RookChessmon, and BishopChessmon. Even armed with the Geo Grey Sword, ShineGreymon proves no match for the Royal Knight either

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. In the battle, Thomas once again comes across his father, Franz, and Relena

Biyomon returns to the Damon household with numerous Fresh and In-Training Digimon in tow. Yoshi and Keenan help out in taking care of them, despite all of the headache-inducing antics of the childish Digimon. Duftmon, under the orders of Yggdrasil, attacks the real world nearby the Damon household

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

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

Craniummon freed BanchoLeomon and took over his place to hold the Digital World from falling onto the human world. It is BanchoLeomon who stops Marcus from getting closer to Yggdrassil and reveals the stunning truth that it is in fact Spencer in the digimon's body while his body is taken over by Ygddrasil. Spencer-BanchoLeomon tells the DATS team how during his past exploits in the Digital World met BanchoLeomon, who both become friends with their fists, and the truth about Yggdrassil's intentions

After BanchoLeomon and Spencer's destruction, Yggdrasil changes to a fighting mode and heads to the Real World to eliminate it. The DATS team follows and engages it in a furious clash, but Yggdrasil easily overpowers them all even at their Burst Digivolution stages. Fueled by their strong bond to protect their beloved ones, regardless of being human or digimon, the DATS all together rise their DNAs into the sky with a cry that is answered by the rest of the digimon on earth and the Royal Knights

Humans and digimon all over town invoke the light of their DNAs to answer DATS' plea for help. When the hearts of all humans and digimon become one, Marcus & Agumon activate Burst Mode and deal the decisive punch to destroy Yggdrasil. Yggdrasil concedes defeat, acknowledging that humans and digimon hold potential for growth as long as both stand together