Arc One

Multiple armies are fighting for control over the digital world, the armies are called Xros Heart, Blue Flare, Twilight and The Bagra Army. They are searching for the 108 Code crowns that will give them control over the zones and whoever gathers all the code crowns becomes digimon king, the digimon king is able to bend the entire digital world to their will. The Bagras army is intent on making the digital world a hellish realm of suffering, Xros heart led by Taiki Kudo (Mikey in the english version) must stop them.

Taiki decides to help Shoutmon and their friends and together they form their own army "Xross Heart" and they leave and travel the Digital world collecting the Code Crowns by themselves. During their travels they meet many friendly digimon who join their cause and they face the evil minions of the Bugra Army including the three head officers Tactimon, Lilithmon and Blastmon.

They also come across rival armies, Blue Flare led by Kiriha and Twilight which is secretly led by DarkKnightmon with Nene being used as a tool for his scemes. After Nene is rescued from DarkKnightmon who created darkness loader so he could digi xros without her help, Nene and her digimon companions also join Xros Heart.

After all 108 Code Crowns were taken Tactimon steals all Taiki and Kiriha's code crowns. Even though Tactimon is defeated by the teamwork of the rival groups Bagramon uses a dimensional warp to take the Code Crowns for himself, this sends Taiki, Akari, Zenjirou, Shoutmon and Tactimon to the human world. With Xros Hearts core members taken care of Bagramon is back with his brother DarkKnightmon as he begins his rule over the Digital World. In the real world Tactimon tries to make havoc before his attmepts are stoped by Taiki and Shoutmon, Shoutmon uses the power of human emotions to digivolve into OmegaShoutmon, defeating Tactimon and returning to the digital world with Taiki.

Arc Two

Upon returning the the digital world Taiki and Shoutmon discover that Bagramon has re-built the digital world into seven kingdoms each ruled by a "Death General" they posses their own darkness loader. Reunited with their Xros Heart allies, Taiki and Nene convince Kiriha to join forces with them and they travel together through the kingdoms to challenge the generals and save the Digital World from the Bagra's armies opression. 

As they continue on their journey, they find out about Nene's little lost brother Yuu. They learn that Yuu has joined DarkKnightmon and the Bagra Army believing that in the digital world no one can die or get hurt, by the time they defeat DarknessBagramon, Yuu realized the truth and joins them. Together with all the digimon in the digi world fighting with them, they finally defeat DarknessBagramon and restores the Digital World.

Arc Three

The Young Hunters Who Leapt Through Time

A year has gone by since Taiki and his friends saved the Digital and the Real World. Digimon from DigiQuartz which is a space between the human and digital world are being influenced by human hearts and are causing trouble in the human world. Also a group of three people called the Digimon Hunters make themselves known and fight the digimon capturing them to make themselves stronger. Eventually Taiki and Yuu with their new friend Taigiru get involved in the Digimon Hunt and the three mysterious hunters. After they show their digimon fighting skills and old Clock maker man tells them that the true purpose of the hunt is to help pick the best person to stand along side the legendary heroes from other universes and fight Quartzmon a really powerful remnent of DarkBagramons data.