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. But Yggdrassil won't go down easily, so Spencer-BanchoLeomon holds him in place and asks Marcus to sacrifice him along with Yggdrassil to save the human world.

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. This determination dawns upon Marcus and ShineGreymon the miraculous digivolution of Burst Mode.

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.

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. The rest of the team are also in cells. Marcus, Thomas, and Yoshi live a normal life, until the Digimon escape and persuade them that they used to be a team. Marcus and the others don't believe this at first, but later regain their memories. Meanwhile, Keenan and the others escape from the cells and try to destroy Kurata, but to no avail. They group together again to defeat another Gizumon that Kurata had sent to attack Marcus. Afterwards, they head over to DATS headquarters to find that it's being destroyed.

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?

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.

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.

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. The collision between both worlds stops, and all DATS are reunited with their loved ones in celebration. But not all is joy, as the Digimon must return to help rebuild the Digital World. Each of the DATS digimon spend their last day on Earth together with their human partners. As the day of the parting comes, Marcus arrives telling Agumon he's coming with it to the Digital World. Five years later, Kristy and Keenan attend middle school together; Thomas received the Nobel Prize for curing Relena's illness; Yoshi has become a police officer; and both Marcus and Agumon have became the number one street fighters of the Digital World.

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.

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....

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. Back to Yggdrassil, Marcus confronts him but is repeled by a force field. It is then that through the revelation of all his friends supporting him, Marcus overpowers Yggdrassil. Just as Yggdrassil lies defeated, Marcus tries to approach him but is interrupted by the sudden arrival of an old friend.

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.

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. When their Bio Digimon forms prove too powerful for the DATS to handle, Sampson and Kudamon appear to help out.

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?

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. Just as ShineGreymon gains the upper hand, Gallantmon and the other Royal Knights show up and defeat him. Yggdrasil reveals himself, but Marcus, determined to not give up, throws a punch at him, only to find the shock of Yggdrasil's true identity: his own father, Spencer Damon.

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. It is then that a badly injured Sleipmon challenges Gallantmon, but at what cost?

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.

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.

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.

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. The remaining DATS are desperately searching for any Digimon survivors, until Thomas appears and much to Marcus' shock and dismay, Thomas orders MirageGaogamon to fight against ShineGreymon.

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. The Royal Knights rebel against Yggdrassil after doubting the motives of their god. In a shocking twist, Yggdrasil discloses that it is the computer which designs and controls all lifeforms in the Digital World at its will.

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.

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.

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 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. When they reach Cherrymon's forest, Kouki, Nanami, and Ivan attack.