While advancing to the next Zone after saving Nene, Xros Heart runs into Arkadimon, a Digimon that catches travelers between Zones and feeds upon their data. Arkadimon turns out to be controlled by Lilithmon in a plot to steal the Xros Loader. While all the others and the Xros Loader are taken away, Taiki is left to drift about the Digital realm alone - until he's found by Wisemon, a Digimon seeking answers to all the mysteries of the Digital World. Wisemon proceeds to tell Taiki all about the history and structure of the Digital World...

Taiki and his friends are caught up in a massive conflict between the Bagra Army, Team Blue Flare led by Kiriha, and Team Twilight led by Nene in the Forest Zone. Nene and DarkKnightmon head for the shrine in the forest to find the powerful sacred Digimon, Deckerdramon, and add him to their ranks. Taiki follows with Shoutmon X4 to save Nene, and Kiriha joins him, but they struggle against DarkKnightmon's overwhelming power. Meanwhile, in response to Taiki's questioning, Nene mentions the name "Yuu"... who could Yuu be?

Taiki's team reaches the Forest Zone, a home of some very powerful Digimon. Akari and Zenjirou wind up separated from Taiki, so Dorulumon and Revolmon set off into the forest to find them. Then Akari and Zenjirou meet Stingmon, the protector of the forest, and Lilamon, who mistakes them for a dating couple. She takes them to a sacred shrine guarded by a barrier to protect them from the Bagra Army. Meanwhile Taiki's team encounters Tactimon and fights him with Shoutmon X4B. They prove to be an even match, but then Kiriha and Nene appear and begin to attack Stingmon and Lilamon...

Taiki's team transports to the Dust Zone, a world full of garbage and scrap, to save Nene. But Taiki's Xros Loader is soon stolen by a group of ToyAgumon, who receive sustenance from a Bagra Army servant, GrandLocomon, in exchange for "mecha" found among the garbage. They then meet a Digimon called Pinocchimon, who takes them to the ToyAgumon - but when Taiki demands his Xros Loader back, Pinocchimon snatches it and disappears!

Taiki's team arrives in the Heaven Zone, a home to many angel type Digimon and a police force so strong that even the Bagra Army can't lay a hand on them. But the president and chief of police, SlashAngemon, and his subordinates are abusing their authority, punishing the smallest of crimes with severe sentences. Taiki's companion Dondokomon is almost arrested for making a racket when he's saved by a local Digimon, Lucemon, but then Taiki and his friends are seized again for a crime they didn't commit, and SlashAngemon prepares to deal them a harsh sentence...

The evil Lucemon absorbs all the dark power sealed in the Heaven Zone, even drawing in Nene in the process. Her partner Sparrowmon tries to save her, but his attacks have no effect and he refuses to cooperate with Taiki and Shoutmon. When Lucemon starts to absorb the Heaven Zone itself and all the Digimon in it, Taiki's team tries to stop him, but can't reach him since Shoutmon X4 can't fly. Sparrowmon finally sees that Taiki's intentions are true and agrees to DigiXros with Shoutmon X4, giving rise to Shoutmon X5!

Lucemon is elected the new president of Heaven Zone, but the citizens' hopes for peace are quickly betrayed. The moment Lucemon is presented with the armband that symbolizes the presidency, he reveals the evil true nature he had been hiding all along! He uses an incantation to split the Zone and release the airborne shrine in which the Code Crown was sealed. Once he obtains the Code Crown, he returns to his true evil form and reveals that he is a servant of Lilithmon. The stunned Taiki is then faced with the appearance of Nene and a dark knight Digimon...

Baalmon, the survivor of the order of Warriors of the Goddess, falls victim to Lilithmon's poison. Taiki begins a ritual to revive him using the Xros Loader, which prevents the others from using it to DigiXros in the battle against Lilithmon's minion. Eventually, Baalmon stops the ritual and sends Taiki to help his companions, saving them but dooming himself to certain death...

As they leave the ruins of the Sand Zone, Taiki's team finds themselves under fire from the Bagra Army's assassin, Baalmon. Then a shock wave from the battle between Kiriha, Nene, and Blastmon sends Taiki and Baalmon tumbling into the sacred underground temple of a goddess. When Taiki extends a hand to the goddess statue he finds there, it emits a light that envelops him, which stuns Baalmon. He reveals that the light is called "the light of the Goddess," and those it shines upon have been chosen as "Warriors of the Goddess."

Taiki and his team arrive in the Sand Zone, which once thrived as an area rich in precious gems. They decide to take a shot at treasure hunting, but along the way they fall into the Bagra Army's underground base and find themselves on the run. They are saved by a treasure hunter Digimon, Revolmon, who then insists that they return the favor by helping him hunt for treasure. They set off into the ruins where the treasure is said to be hidden, but are impeded by various traps and pursued yet again by the Bagra Army. At last they reach the final chamber, where the mysterious Digimon Pharaohmon awaits them...

With Taiki unconscious from exhaustion, Zenjirou leads the counterattack against the Bagra Army in his place. Meanwhile Bastemon keeps a constant watch over Taiki, leaving Akari feeling a bit like a third wheel. A dejected Akari is then lured by a vision of her mother in a mirror, which turns out to be the magic of Lilithmon telling Akari she'll help her return to the human world in exchange for the Lake Zone's Code Crown. As Akari searches for the Code Crown, Lilithmon awakens a secret weapon to launch her ultimate attack on the castle...

Xros Heart arrives in the Lake Zone, where Taiki saves Knightmon, a Digimon that had fallen into a frozen lake amidst a Bagra Army attack. A grateful Knightmon takes Taiki to the castle to have him made the captain of its knights, but the princess Bastemon has already chosen someone for that position: Taiki's rival Kiriha! The two of them must join forces in order to turn back the Bagra Army attacking the castle, but the exhaustion of the battle finally gets to Taiki in the end...

Tactimon arrives in the Magma Zone and tells Taiki a shocking story of Dorulumon's past: he used to be a prodigal warrior in the Bagra Army who conquered many Zones as Tactimon's right hand man! He calls Dorulumon a traitor, but Taiki still chooses to trust him. They eventually escape from their cage and face AncientVolcamon, who has grown even stronger after absorbing his own allies. Dorulumon and Shoutmon DigiXros to fight him and try to return peace to the Magma Zone for good!

The Bagra Army has been forcing the Digimon of the Magma Zone to search for the Zone's Code Crown. Taiki fights to rescue them, but he's met by a Digimon of overwhelming power, AncientVolcamon! Taiki and his companions let themselves be arrested to find out where the prison is, and team up with the prisoners to attempt an escape. However, when the Bagra Army's leader Tactimon hears that Taiki and Dorulumon have been captured, he appears to confirm the story personally - and tells Taiki's team all about Dorulumon's past...

After defeating the Bagra Army again, Taiki's team heads to the Magma Zone. When the team is attacked by more Bagra troops led by DeathMeramon, Dorulumon dashes in to save them. Taiki asks Dorulumon to travel with them, but he refuses and leaves again with Cutemon. Later Taiki learns that the local Digimon are being forced into slavery by the Bagra Army and sets off into a cave to rescue them, but he's found by the Bagra Army and the giant volcano Digimon, AncientVolcamon!

Taiki and his team have acquired another Code Crown as well as DigiMemories, cards containing the data of legendary Digimon - but now the Bagra Army has them surrounded! Kiriha hears this and offers to save Taiki's team in exchange for the DigiMemories, but Taiki refuses and summons the DigiMemory of MarineAngemon in order to reach the enemy ship. There he attempts to rescue the chief of the Island Zone, Archelomon, who is held captive by the Bagra Army...