Taiki Kudou is an uncommonly good-hearted seventh grader who "can't turn his back on" someone in a pinch. One day he follows the voice of a Digimon in need and is granted a Xros Loader, a device that allows him to give Digimon added strength through the command "DigiXros!" Taiki becomes a General and is sent with his two friends to the Digital World, which is currently ravaged by war between the Digimon. Taiki and Shoutmon, the Digimon he saved, use the Xros Loader to build up a new army and join in the battle against the attacking Digimon!

After Taiki defeats the Bagra Army's champion, MadLeomon, by uniting Shoutmon X2 and Dorulumon through a DigiXros, a golden fragment descends from the sky before his eyes. A mysterious girl named Nene Amano appears and tells him it is a fragment of the Code Crown, an object that allows its owner to control the Digital World. Following Nene's instructions, Taiki places the Code Crown in his Xros Loader and travels to another Zone, unaware that the Bagra Army is taking secret measures to obtain the Code Crown as well...

Taiki and his team arrive in the Island Zone intent on finding more Code Crown fragments. Meanwhile, the Bagra Army learns that the Island Zone's Code Crown is inside the belly of Whamon, the great Digimon who carries the Island Zone on his back, and tries to feed him explosives to stun him so they can steal it. Taiki and Shoutmon dive into Whamon's belly themselves to find the Code Crown first, but the Bagra Army's Flymon squad is close behind...

When Taiki visits Shoutmon's home, the Village of Smiles, he sees that war has plunged the Digital World into chaos. Shoutmon begs Taiki to stay and fight the enemy with him, but Taiki's reply creates a rift between the two. Meanwhile, the Imperial Bagra Army launches another attack on Taiki and his friends...

Taiki has decided to stay with Shoutmon and his other Digimon friends, but when the Bagra Army learns that Taiki can make Digimon DigiXros using the Xros Loader, they initiate attempts to eliminate him. Meanwhile another boy who uses a Xros Loader, Kiriha, shows up and tries to coerce Taiki into working for him...

The truth is revealed and it is up to Tagiru and Arresterdramon to save the digital world and the real world. But will the power of Brave Snatcher be enough to stop Quartzmon?

Legendary Digimon Heroes are assembling to battle against Quartzmon turning the human world digital. But one more hero is needed and Tagiru has to fight the other Hunters for the spot.

Tagiru and Hideaki follow rumors of a shining golden stag beetle in the mountains, launching a Hunt when they suspect Digimon involvement. Meanwhile, Tagiru's insect-loving classmate, Kaneda, is convinced that Tagiru is only trying to capture the new stag beetle species for profit, and won't let him out of his sight. He ends up in DigiQuartz with Tagiru and Hideaki as they search for the truth behind the shining golden stag beetle...

When kids begin to disappear in large numbers, Taiki and Yuu suspect a Digimon's involvement and set out to investigate. Tagiru then returns from a failed Digimon Hunt and meets Bakomon, a Digimon who has been inviting children to a theme park called DigimonLand. Tagiru and Gumdramon follow him there and find many other Digimon working hard to make children happy. They decide to put off their Hunt and join the fun, but the good times are cut short when Tagiru's friends try out the special attraction and are not seen again...

Hiroya strives for the top ranking in the card game Sea Monster Cards, but he's not faring well without any strong rare cards. Then he meets KnightChessmon, a Digimon who promises to grant his wish. Later, Tagiru and his friends hear rumors of kids being dragged to another world where their rare cards are stolen. Suspecting a Digimon's involvement, they head to a card game tournament to find the truth...

Tagiru and company are enjoying a day of fishing at the beach when a Digimon Hunter, Mizuki, and her partner, Submarimon, appear. Mizuki, also a treasure hunter, tells them of a sunken treasure in a cave in DigiQuartz that she can't reach because it's guarded by an evil Digimon called Dagomon. She asks Tagiru and the others to Hunt Dagomon for her, so they follow her to the undersea cave, where they find much more than just Dagomon...

After being teased by his classmates about his drawings of UFOs and UMAs, Shouta meets the Digimon Ekakimon that has the ability to turn drawings to reality. With Shouta’s powerful imagination, the school is in danger of being overrun by fearsome monsters.

When the thief and master of disguises, Betsumon, shows up, Tagiru wants to Hunt him, but Gumdramon is unwilling. Even Ryouma and the other rival Hunters have fallen victim to Betsumon's tricks, so Tagiru and company team up with them to stop him. Encouraged by Taiki, Gumdramon at last faces Betsumon in battle and reveals that the two of them used to be partners - but Betsumon no longer remembers him. Can Gumdramon recover his lost friendship with Betsumon?

An old phone rings and voice on the other end is asking for help. Tagiru and Yuu go to check it out and run into the ghost hunter Kaoru. Is the disturbance caused by a Digimon or something from the other side?

The Digimon Phelesmon, has promised to make the new kid Makoto popular. Phelesmon is hypnotizing the students and it’s causing him to grow stronger. With Tagiru and Taiki the only ones not hypnotized, are they strong enough to stop him?!