After a tutorial fight with an Otamamon, Marcus Damon and Agumon take on Tylomon who is sinking ships in the area of Walter Island. After Tylomon is defeated, Creepymon appears and defeats GeoGreymon. When Creepymon tries to take down Marcus and Agumon, Creepymon notices Marcus' Digivice iC and flees. Yoshino arrives to recall Marcus and Agumon to DATS HQ. Meanwhile, a girl named Yuma ends up kidnapped by two DemiDevimon and her Renamon arrives late.
At DATS HQ, Commander Sampson and Kudamon report that 5 children have gone missing throughout the world. He sends Marcus and Yoshi to Sneyato Forest to rondezvous with Thomas and take down Bakemon who is tampering with Earth's electricity. When they catch up with Thomas, a fight ensues with Bakemon. During battle, Bakemon Digivolves into Myotismon and a mysterious transmission tells them how to defeat Myotismon. After that is done, the DATS members return to DATS HQ and discover that Thomas' old friend Tsukasa Kagura has transferred here and was the one who gave them the tactics to defeat Myotismon. He also tells them that his sister Yuma has gone missing.
Arriving at Rage Caverns, Kagura warns the DATS members that their Digimon may not Digivolve into the same Digimon due to the activity in the Dark Area. After a series of earthquakes, the DATS members find the source to be Belphemon. They defeat Belphemon and a boy is rescued from some of Belphemon's data with the Sloth Code Key in his possession. Just then, a private investigator named Kosaburo Katsura and his Biyomon appeared and claimed the Sloth Code Key. He disappears as Kagura prepares an immediate evac for the DATS members to bring the boy back. Meanwhile, Creepymon is seen at the door to the Dark Area as a mysterious person approaches him.
A flashback has Misaki Nitta announcing to Yoshino and Commander Sampson that he is leaving DATS due to he injured a criminal with his Digimon Partner. This event was told to the other DATS's members. Yoshino reveals to Kagura that Kosaburo interfered with her past missions when it came to the info of the Sloth Code Key.
After Keenan Crier joins the team, another huge Digimon signature is detected at Mirage Museum. Kagura tells them that missions will be done in fours now with the fourth being the backup player. Thomas mentions that Mao Digimon don't fit the category of the other Digimon Levels. After footage is shown with what might be Yuma and Lilithmon on an island, the Mao Digimon Barbamon appears and fights the team. He is defeated and a girl is rescued from his data with the Greed Code Key in her possession. Kosaburo and Biyomon appear and claim the Greed Code Key. He disappears as Kagura prepars an immediate evac for the DATS members to bring the girl back.
Back at DATS HQ, Kagura tells the team that his sister Yuma was nicknamed "monster girl" cause she can talk to "monsters." Kagura identifies the footage from the Mirage Museum to be an SOS from Livilus Island. The team is dispatched there to answer an SOS which turned out to be from Renamon who collapsed near them. After recovering, Renamon tells the DATS members that Yuma has become part of the material that comprises the Mao Digimon Lilithmon. They encounter Lilithmon who insults Yoshino and a battle begins. After Lilithmon is defeated, Yuma returns to normal. Gaomon manages to attack Biyomon before Kosaburo can claim the Lust Code Key. When Kosaburo digivolves Biyomon into Birdramon, Renamon uses what she has left to heal the other Digimon. The DATS team defeats Kosaburo and Birdramon, but they escape. Kagura arrives since he lost contact with the DATS members and tells Yuma that they will treat Renamon at DATS' facilities.
At the Sea Precipice Jerapilus, Kosaburo makes contact with his client, and tells him that DATS has the Code Key of Lust. Despite this, he transfers the two Code Keys, Sloth and Greed, to his client. The mysterious person gives the 'investigator' the money agreed for the cards, and leaves with the fact that the event "ends their relationship." When Kosaburo and Biyomon talk about what to do with their pay, Creepymon arrives and attacks the two.
The DATS team arrives at the Digital Dungeon and ensue in a battle with Beelzemon. When they defeat Beelzemon, a boy is freed. The teams finds the Code Key of Gluttony in his possession.
When the DATS team arrives at the Sea Precipice Jerapilus, they ensue in a battle with Leviamon and defeat him. They also find a silent cool girl who had the Code Key of Envy. Kagura arrives to claim the Code Key. An injured Kosaburo arrives to tell them that Kagura was the unknown client, since he planted a tracking device in Kagura's pocket. As the tracking device goes off, Thomas finds the Code Keys in Kagura's pockets.
Kagura then tells Thomas that his henchmen, DemiDevimon and Devimon had kidnapped Yuma and her friends, the other missing children, because he wanted them to become the confused sins of the Mao Digimon. Two DemiDevimon snatch the Code Keys from Yoshi. After that, they battle two DemiDevimon and two Devimon and win. After the battle, Kagura disappears with all Five Code Keys.
Commander Sampson calls and the DATS team tells him everything, much to their surprise.
After Kosaburo joins the team, they find that Kagura is using the Code Keys to unlock the seal to the Cho-Mao Digimon, Lucemon. The team is sent to a forest where the Digital World begins to fall apart. In a re-match against Creepymon, the DATS team emerges as the victor. A gate to the Real World appears, which Creepymon flies through. He drops a Digivice iC, which the team identifies. Yoshino asks what he means by "going home." Yuma then joins the five.
In the Real World, after defeating some Digimon that were attacking the Real World, they find Creepymon again for a final battle against him. After he was finally defeated, it is revealed that Nitta was missing because he was used as part of the material to create Creepymon. Nitta regained awareness and accepted the fact that he had become a Digimon. The Digivice (which Yoshi had picked up), however, did not belong to him, but to his daughter. He wanted a way to see his daughter again, making the Digivice appear. He was to become her Digimon. Because the device locked on to his Digital signature, he could never go back to being a human even if he was defeated. Before Nitta vanishes, he tells Yoshino to tell his daughter that he loves her. He also reveals that Kagura has the Code Key of Wrath, thus he has all the Code Keys (Wrath, Gluttony, Greed, Sloth, Envy and Lust) to unseal Lucemon.
Kagura unseals Lucemon. When the DATS team asks Kagura his motives, he heatedly explains how his pride at being a genius was wounded when Thomas became his underclassman and made him look merely average. Kagura had vowed from that day to surpass Thomas at any cost. Kagura shows the team a Digivice iC of his own creation, and uses it to infuse Lucemon with his own Digisoul Charge, fully awakening the Great Demon Lord Digimon. Kagura claims he is now like a god himself. Yuma tells her brother that what he's doing isn't right. Kagura replies that what he's doing was in order to become the ideal brother for Yuma. At this, Yuma breaks down, crying. Marcus becomes angry and tells Kagura that the most important thing to protect is family, a point that he will beat into Kagura if necessary. Kagura decides that since DATS is in his way, they can simply become more material for Lucemon's body, and attacks them.
After Lucemon is defeated, he absorbs Kagura (revealing Kagura himself as the final Code Key of Pride, the first six were to free him from his physical state of frozen imprisonment in the Dark Area itself and the Code Key of Pride was necessary for Lucemon to leave the boundaries of the point in the Dark Area where he was trapped.) and retreats. After a group of Mega Digimon are defeated, the DATS team confront Lucemon. After beating him, he changes into his Demon Lord form. When the six emerge the victor, Kagura is freed from Lucemon and lays on the ground, asking for forgiveness.