The story begins with a seventh-grade boy named Taiki Kudō dreaming of commanding a Digimon army. The next day, Taiki spots a red creature flickering in static and hears a mysterious voice which presents him with a Xros Loader, into which the creature is absorbed. He and his friends, Akari Hinomoto and Zenjirō Tsurugi, are then sucked into a portal to the Digital World, where they are attacked by MadLeomon and his troops. The group is rescued by Ballistamon, Starmon, the Pickmon, and the mysterious red creature: Shoutmon. After Taiki and his Digimon companions fight back against MadLeomon and his troops, MadLeomon absorbs some Chikurimon, Troopmon, and Mammothmon to become Armed MadLeomon. Taiki uses his Xros Loader to allow Shoutmon and Ballistamon to DigiXros into a more powerful form. After injuring Armed MadLeomon, Shoutmon then uses the DigiXrossed Starmon and Pickmon, in the form of the Star Sword, to strike down Armed MadLeomon with a finishing blow.

The kids go with Shoutmon to his home, Village of Smiles, where they are thrown a party. Soon after Taiki decides to try to leave the Digital World and return home since he accidentally dragged Akari and Zenjirou with him, causing Shoutmon to become upset. The humans and digimon go their separate ways but MadLeomon attacks the kids once more, combining with Orochimon. Shoutmon comes to their rescue and with the help of Taiki to DigiXros, becomes Shoutmon X2 and defeats MadLeomon, causing the evil digimon to retreat. Nene is seen watching Kiriha and Taiki individually, evaluating their fighting skills.

The Village of Smiles is suffering from the threat of the event known as "Day of Rising Ground." The human boy known as Kiriha appears and informs Taiki and the others about what is happening, offering his help but only if Taiki joins his side and serves under him. He mentions something about the "Code Crown" as well. Refused, Kiriha uses DigiXros on MailBirdramon and a Golemon to fight Shoutmon and his friends. However MadLeomon's forces decide to attack the village as well...

The mysterious and beautiful girl known as Nene explains to Taiki and the others about the Code Crown. It is revealed that what they have is but a fragment of a larger piece and that there is a fragment for every Zone. Using the fragment's power to do a Zone Transfer, Taiki's Xros Heart army ends up in the Island Zone, surrounded by a vast ocean. However they quickly find out that this is not an island paradise as the Bagura Army's influence is in this zone as well.

Captured by Neptunemon, Archelomon is forced to give up the whereabouts of the Code Crown. In order to protect the Code Crown, Taiki and the others head into the stomach of a gigantic Digimon, Whamon. There, the group, as well as the Bagura Army, wage battle inside Whamon. Later, they find DigiMemories of legendary digimon under Whamon, and using them, they summoned legendary digimon Leviamon.

Teams Xros Heart and Blue Flare must protect KingWhamon and the Island Zone's Code Crown from Neptunemon's Seadramon army. Taiki realizes that a DigiMemory can only be used once and summons the memory of MarineAngemon to fight off the Seadramon army. They then take on Neptunmon himself....

Team Xros Heart arrives in the Magma Zone where they decide to relax a bit in the hot springs. Their time for relaxation is cut short when SkullMeramon and some Meramon of Bagura Army shows up. Cutemon and Dorulumon comes to their rescue once more and Cutemon reveals that he is looking for his parents. Also it seems that BlueMeramon in the Bagura Army knows Dorulumon...

To prevent AncientVolcamon from destroying the cave and killing the prisoners, Taiki issues a surrender from Team Xros Heart. He then hands over a fake version of his Xros Loader and the gang is lead away to a cell where they hope to find Cutemon's parents. There they plan an escape unknowing that Tactimon has arrived to the Magma Zone, with an unexpected revelation.

Tactimon attacks Team Xros Heart and captures Dorulumon and Taiki, ordering their execution. Meanwhile Nene informs Kiriha of Taiki's capture and he comes to fight Tactimon. While Tactimon is distracted by Mailbirdramon and Kiriha, BlueMeramon helps Taiki and Dorulumon to escape along with the rest of Xros Heart. The group then learns more about Dorulumon's involvement with the Bagura Army while they look for Taiki's Xros Loader.

Arriving in the Lake Zone, Team Xros Heart quickly discovers that the Bagura Army is present thanks to IceDevimon's frozen victims. After rescuing a drowning Knightmon, Taiki and the others are introduced to the ruler of the castle of the Lake Zone: Persiamon. Meanwhile IceDevimon and his troops attack but when they fail and retreat, the general Lilithmon appears to take over. She then reveals the plan to thaw out a frozen powerful and dangerous digimon.

Overdoing it during battle, Taiki passes out and Persiamon takes over to care for him. However Akari becomes sad and jealous since that is usually her job. Unfortunately Lilithmon seizes the opportunity to turn Akari's emotions against her and control her, forcing Akari to find the fragment of Code Crown and bring it to her. Meanwhile as Taiki recovers, Lilithmon also unleashes the powerful digimon Daipenmon who nearly wipes out Taiki's forces that Zenjirou is leading. At the very end Nene appears before Kiriha, saying she has decided to team up with him, revealing that she wields a black Xros Loader.

Heading into the Sand Zone, the Fusion Fighters fall prey to the heat and the Bagra Army. Saved by Deputymon, they are forced to go treasure hunting at gunpoint, while the last of the Three Generals, Blastmon, roams the Zone.

The battle between Blastmon and Nene and Kiriha's forces continue. Meanwhile as Team Xros Heart investigates the commotion, they are attacked by Baalmon who accidentally reveals an old Digimon goddess statue that has been buried. While fighting, Blastmon causes the ground to collapse, making Taiki and the statue to take a tumble deep underground, separating the kindhearted general from his friends. Baalmon then appears before Taiki and says Taiki has been blessed by the goddess and is now her warrior. In response, Baalmon helps lead Taiki from the underground while enlightening him about the past of the Sand Zone and the goddess warriors. Eventually Taiki learns more about Baalmon himself and his tragic past...

After Baalmon is fatally wounded by Lilithmon, Taiki is instructed by Pharaohmon to use the Sand Zone's Code Crown which rises a pyramid that carries Team Xros Heart and Baalmon away from Lilithmon and her SkullScorpiomon army. Taiki uses his DigiXros to summon the statue of the Digimon Goddess to begin healing Baalmon's wounds. Meanwhile Lilithmon's forces try to break into the pyramid and Team Xros Heart all band together to fight while being unable to Digi Xros.

In Heaven Zone arena, a crowd of Digimon are watching a Gargoylemon and GuardiAngemon (commanders of Heaven Zone's Police) executing a Puttimon who broke laws. Meanwhile, Xros Heart arrives at the Zone and amaze by the surrounding. Later, Taiki falls off a cliff but is saved by Shakkoumon. Dondokomon drums disrupting a Pucchiemon orchestra and gets in trouble with a police Piximon. Taiki tries to stop the argument caused by Dondokomon as Lucemon shows up to clean the mess. After the argument is off, Lucemon tells Taiki and the that Gargoylemon is a member of the Heaven police. Lucemon then takes them on a balloon tour, but Dondokomon knocks down a sculpture. Gargoylemon arrives and arrests Dondokomon, Taiki, and Shoutmon. Moments later, Taiki teammates and Lucemon visit the police department where they are told that Dondokomon is being interrogated. Ballistamon ends up busting Taiki, Shoutmon, and Dondokomon out which alerts the rest of the force.

As GuardiAngemon holds a coronation for Lucemon, Shoutmon has an encounter with Shakkoumon in the library after Lucemon leaves. When Lucemon arrives for his coronation, it is crashed by Shakkoumon who is really the administrator of the election. Lucemon uses the Heaven Zone's Presidential Armlet to split the Heaven Zone unleashing a floating building in order to gain its Code Crown. Lucemon than Digivolves into Lucemon Chaos Mode and reveals that he is actually working for Lilithmon. When Shoutmon tries to attack Lucemon, he ends up zapped upon the arrive of Nene and DarkKnightmon. She releases Sparrowmon as she and DarkKnightmon head to the floating building where a dark energy ball which also appear with the Zone's parting as it is corrupting the Heaven Zone's inhabitants. Before Lucemon takes off, he is grabbed by Ballistamon and then attacked by Dorulumon only for him, Ballistamon, Starmon, and the Pickmons to be knocked away.

As the dark energy ball engulfs Lucemon Chaos Mode and Nene, Sparrowmon tries to grab Nene but fails as the energy digivolves Lucemon into his Shadowlord Mode with the girl trapped in the Gehanna sphere. As Lucemon takes off, Sparrowmon attacks him to rescue Nene as Shoutmon ×4 and Beelzebumon also involving in the fight too. But neither the Xros Heart Digimon or Sparrowmon could stop Lucemon as he siphons all the dark energy from the Heaven Zone's darkness-infected citizens, growing bigger as a result while a Monitamon informs DarkKnightmon on the current situation. While Xros Heart regroups to figure out how to defeat Lucemon, Nene reflects on the time when she was with Sparrowmon. Sparrowmon wakes up in Xros Heart's care as Lucemon starts to absorb the Heaven Zone as Shoutmon ×4, Beelzebumon, and Shakkoumon are unable to stop him. Without the help of DarkKnightmon, Sparrowmon tries another attempt at Gehanna with Taiki using the Patamon DigiMemory so Shoutmon ×4 to support her.

While traveling to the next zone, Xros Heart end up falling from the skies into the Forest Zone. Beelzebumon, Akari and Zenjirō has split fron Taiki and his remaining team members after the fall. Taiki then looks for Akari and Zenjirō by sending Dorulumon and Deputymon to perform the task. Akari's side encounter with Stingmon who launches an attacks on them but stopped by Lilamon and later reveal themselves as the guardians of the Forest Zone's deity that sleeps within a sacred temple. Just then, Taiki find themselves surrounded by Kongoumon and his army of MegaKabuterimon. He then DigiXros Shoutmon into Shoutmon ×2 and brings out Knightmon and the PawnChessmon to fight their rival with Tactimon arrives. Dorulumon and Deputymon are managed to locate Zenjirō and Akari and Beelzebumon follows them, leaving Zenjirō and Akari behind which later they encountered with Kiriha and Nene.

Nene and DarkKnightmon pursue the light that Stingmon is in revealing that he is then healed by the Forest Zone's deity Deckerdramon. Outside the temple, Lilamon mentioning a dance ritual called the Love Love Dance which will open a gateway while Taiki goes after Kiriha and drawing him back to the ruins. In front of a crowd of digimon, Zenjirō and Akari are forced to perform the embarrassing dance and it is working, calling Deckerdramon’s attention to open the gateway. Taiki and his teammates catches the light with Kiriha, Sparrowmon and Monitamon following him while Beelzebumon and some others stay behind to fight Kongoumon. Nene and DarkKnightmon appear before Deckerdramon in an attempt to recruit him and gain the Zone's Code Crown. The Xros Heart arrives and DigiXrossing Shoutmon into Shoutmon ×4 along with Kiriha's MetalGreymon to fight with DarkKnightmon.

The wave of darkness that Taiki is ensnared by is revealed to be DarkKnightmon's action in an attempt to recruit Taiki. It turns out that Taiki pure heart revokes the dark energy of an orb stored by DarkKnightmon, leading the discards of Taiki off a tower. Luckily, Taiki is saved by Akari and Dorulumon, though his Xros Loader is stolen by a Garbagemon who escape onto a Kettle the Trailmon with his teammates who consist a groups of MetalMamemon and ShadowToyAgumon. During the pursuit, Taiki, Shoutmon, and Dorulumon end up caught between the train tracks as different Trailmon pass by, that is sending trashes all around. Taiki then has an encounter with Puppetmon. Through Puppetmon, the gang soon learns about the tyrant Digimon GranLocomon is ruling the Dust Zone. When Taiki mentioned about Xros Loader, Puppetmon's behavior was turn rapidly by offering himself to Taiki for searching it.

Xros Heart are forced to fight DarkKnightmon and Kiriha, managing to escape them with Puppetmon's help. Later, Sparrowmon arrives, persuading Taiki to save Nene along telling him DarkKnightmon's intention to form a Darkness Loader for his own sake. Later, DarkKnightmon offering Lilithmon to work together to finish up the Xros Heart. Deciding to save Nene, Taiki is stopped by Kihira but Taiki managed to snap him out of DarkKnightmon's control. Kihira instead team up with Shoutmon ×4 to battle against DarkKnightmon and Lilithmon along with their army. Taiki and Sparrowmon managed to save Nene and returned to the battle field and soon DigiXros Shoutmon into Shoutmon ×5 and wipe out the Guardromon. Puppetmon later throws a MetalGarurumon DigiMemories at Taiki and he activates it and with the power of MetalGreymon's Cyber Launcher, Taiki razes the remaining Tankmon.

After a brief talk with Taiki, Nene discovers that her Black Xros Loader no longer works and collapses. Needing to get her some help, the team decide to take Nene to the Monitamon's home in the Shinobi Zone. However, whilst travelling between zones, the group are attacked by Arkadimon and Taiki ends up getting separated from the rest, who thrown away into a dark space. Soon, he is pulled into a strange book and met with Wisemon who explains to him about the Code Crowns and the strange occurrences in the human world. Meanwhile, Shoutmon and the others are trapped in Arkadimon's nest and preventing Arkadimon from consuming them. Taiki soon makes his way in searching for the rest. As Taiki runs into trouble, Wisemon appears to assist Taiki, who then regains his Xros Loader and DigiXros Shoutmon into Shoutmon ×5 while making sure the others are safe.

As Xros Heart meet the Monitamon of the Shinobi Zone, who have been following their exploits through the Monitamon under Nene, they learn that Blastmon's general Musyamon has taken over most of the Shinobi Zone. They visit a Monitamon training camp and learn that the Monitamon Princess has been taken hostage by Mushamon, who wants the Code Crown in exchange. Just then, a Shurimon arrives and tries to attack the Monitamon Elder, but leaves in exchange for a Samurai DVD. After trickily getting everyone up a cliff, Zenjirō falls off but is saved by a group of Etemon. They are then led to the lair of Karatenmon, who will only give up the Code Crown if someone can make him laugh. Everyone puts on their own acts to make him laugh such as Shoutmon's DigiXros with other Digimon, but with no result. However, Nene, who has lightened up a bit more, joins Akari in a comedy sketch which successfully makes Karatenmon laugh.

Wanting to impress Nene, Zenjirō offers to sneak into Musyamon's base, taking Dorulumon, a trio of red Monitamon and the Rare Star Sword with him whilst Taiki and the others hold off Shurimon's army (consisting of Gaiomon, Asuramon, and a bunch of Igamon) using an Impmon DigiMemory in the process. As Zenjirō gets further into the base, he notices the desperate situation that Taiki and others are facing and becomes more determined to sneak into the base while Dorulumon holds off the guards. Zenjirō then faces against Musyamon while Nene's Monitamon save the princess. When Zenjirō's words and situation is broadcast to the rest, Nene flies over to the base to save the red Monitamon from being killed by Mushamon. Her Xros Loader soon transform from black to lavender and DigiXros the red Monitamon into Hi-Vision Monitamon, who distracts Musyamon. Taiki soon DigiXros Shoutmon into Shoutmon ×5 to face the opponent.

In the Disc Zone, Kiriha has just obtained the Code Crown from Mercurymon and encountered with Blastmon where soon they started a battle. Xros Heart arrived and discovered the destruction made by DeckerGreymon (Kiriha's newly DigiXrossed Digimon) and Blastmon. Taiki tries to intervene the battle with Shoutmon ×4K but undesirable result occurs, as a sudden Xros open happens to Shoutmon ×4K, resulting the battle to become even worst. Just then, the ground collapses sending Blastmon out of the battle and separating Shoutmon, Greymon and MailBirdramon from the others. Realizing Disc Zone is continuously collapsing, Taiki fail to persuade Kiriha to save the Zone. Soon, a Bulbmon is unleashed by Blastmon to extend the chaos. Reunited with Taiki, Shoutmon is again forms into Shoutmon ×4K, which later starts to weaken again and Bulbmon almost crushes him. Greymon unexpectedly steps in to assist him by flipping Bulbmon over together and destroy him.