Exclusive characters include Yuma Kagura, who has a Renamon as her partner; Kosaburo Katsura, a cocky private investigator who has an extremely clumsy, male (changed to female in the US release) Biyomon as his partner; Tsukasa Kagura, who is Yuma's older brother, and the new DATS technician, who graduated from the same academy as Thomas; Masaki Nitta, who is said to be a part of DATS' past, but is currently missing; and Manami Nitta, Masaki's daughter.
At DATS HQ, Commander Sampson and Kudamon report that 5 children are going missing throughout the world. He sends Marcus and Yoshino 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 there 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 named Wyiu 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 harmed a criminal with his Digimon Partner. This event was told to the other DATS 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 named Florda is rescued from his data with the Greed Code Key in her possession. Kosaburo and Biyomon appear and claimed the Greed Code Key. He disappears as Kagura prepares 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 dispacthed 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. Meanwhile at the Sea Precipice Jerapilus, Kosaburo makes contact with a mysterious person telling him that DATS has the Lust Code Key and transferes the Sloth and Greed Code Keys to him which ends their relationship. Just then, Creepymon arrives and attacks Kosaburo and Biyomon.
The DATS team arrives at the Digital Dungeon and ensue in a battle with Beelzemon. When they defeat Beelzemon, a Western Boy named Yèhèrta was freed and had the Gluttony Code Key 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 named Yigua who had the Envy Code Key. Kagura arrives to tell them that he has have lost contact and to claim the Code Key. An injured Kosaburo also arrives to tell them that Kagura was his recent client. As he planted a tracking device in Kagura's pocket to find out who was his client. As the tracking device went off, Thomas asked Kagura to empty his pockets and found the Code Keys. Kagura laughed and told Thomas that his henchmen the DemiDevimon and Devimon had kidnapped Yuma and her 4 Friends (who happened to have been the missing children), because he wanted them to become the confused sins of the Mao Digimon. 2 DemiDevimon snatched the Envy Code Key from Yoshino. After that, they battle 2 DemiDevimon and 2 Devimon and win. After the battle, Kagura disappears with the Code Keys.
Commander Sampson calls and the DATS team tells him everything, much to their surprise.
After Kosaburo joins the team, they reveal 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 was beginning to fall apart. They fight Creepymon and win. Suddenly a gate to the Real World appears and Creepymon was badly hit and almost dies. Plus he flies through it saying "I'm going home". He drops a Digivice iC and the team identifies it and Yoshino asks what he means by "Going home."
After Yuma joins the team, it is later revealed that Nitta was missing because he was used as part of the material that was used to create Creepymon. He had some how regained his self and accepted the fact that he had become a Digimon. The Digivice however was not his, it was his daughter's. He said he wanted a way to see his daughter again and the Digivice appeared out of nowhere. He was to become her Digimon or Father as being a Digimon. However since the device locked on to his Digital signature, he could never go back to being a human even if he was defeated. Before Nitta dies, he tells Yoshino to tell his daughter that he loves her. Nitta then vanishes along with the Digivice.
Then after, Kagura summons Lucemon. Yuma tells Kagura that this is all wrong. After Lucemon is defeated, he absorbs Kagura and leaves to the deeper parts of the Dark Area. After you defeat some Mega Digimon (who were all Lucemon's minons in the Dark Area because they were Dark Area Administrators), the DATS team confront Lucemon. After beating him, he changes to a stronger form, his true body, Lucemon Shadow Lord Mode. Once you defeat his true body, Kagura is freed from Lucemon and lays on the ground asking for forgiveness.