工藤大树是看到有困难的人就无法放著不管的国中生。某天因为他这样的个性拯救了一个谜样生物，但也因此将两个朋友阳本明里及剑善次郎给捲入了异世界。

到底这三人的命运会如何呢？大树所拯救的谜样生物又是什麽？紧张刺激的异世界冒险即将展开！

咆哮兽们所住的微笑之里被巴古拉军给袭击了！虽然咆哮兽请求大树们一起拯救村子，大树却因为要和明里、善次郎一起回人类世界而拒绝。到底咆哮兽会採取什麽行动呢？大树他们能顺利回到人类世界吗？在异世界的冒险即将揭幕！

在巴古拉军干部战策兽的指示下，疯狂狮子兽命令鑽地兽刺激微笑之里的地底，使地底长出巨大的竹笋，有惧高症的善次郎一口气被抛到空中！就在此时，出现在大器面前的是人类少年桐叶和少女宁宁！这两人会是敌人还是朋友呢？

得到地区的支配者证明──代码王冠晶片的大树们，来到下一个地区。为了拯救被巴古拉军所侵略的岛屿地区，大器和咆哮兽等人组成的队伍Xros Heart挺身而出，但在八爪鱼兽的攻击下大树们却跌落海中！在水中无法自由行动的咆哮兽该如何是好呢？

为了得到在巨鲸兽肚子裡的代码王冠晶片，巴古拉军们与大器们纷纷潜入巨鲸兽的肚子裡，然后咆哮兽却在此时被皇蜂兽的毒针给刺到了！代码王冠晶片究竟会落入谁的手中？传说中的宝物又是什麽？在波澜万丈的战斗中，小乌龟兽所下的决心是…！

就在大器们打算用代码王冠晶片，向巴古拉军换回被抓走的海龟兽时，桐叶又再次出现在大树们的面前！拒绝桐叶所提出协助的大树面前，又出现了多鲁路兽！到底桐叶的提议是什麽？大器们是否能平安救出海龟兽呢？可爱的传说中数码兽登场！

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.

As the Disc Zone collapses, Taiki quickly transfers all the Digimon over to Shinobi Zone. However, fragments of Blastmon cling onto some of them and attacks them as night as revealed to Taiki by Wisemon. Beelzebumon soon arrives and DigiXros with Deputymon to destroy the pseudo-Blastmon. Later, Shoutmon gets some personal training from Ballistamon and Beelzebumon in order to prove himself as a strong Digimon, able to become the Digimon King. A Digimon named Tuwarmon appears during the training and informing them that Blastmon's arrival to the zone before leaving. As Blastmon arrives, Shoutmon ×4B fights against him, pledging to protect the people around him. Shoutmon ×4B is then further DigiXros into Shoutmon ×5B and defeated Blastmon while gaining most of his Code Crowns. Meanwhile in a now-ruined Disc Zone, Tuwarmon revealed to be DarkKnightmon's spy, planted into the Bagra Army under the guise of Damemon.

Taiki founds and rescues the digimon, known as Spadamon with Cutemon healing him. Spadamon explains that the Sweets Zone has been taken over by the Bagra Army's Matadormon, forcing the patissiere to prepare desserts for him. In order to save them, Xros Heart enters the Sweet Zone and persuaded the group of Monzaemon which they encountered that Akari is the best patissiere in the Digital World. While Nene and the Monitamon concentrate on rescuing the imprisoned patissiere, the Xros Heart enter a kitchen colosseum where they meet with the top chef WaruMonzaemon, Matadormon private chef, and took down a challenge in order to make Matadormon reveals himself. Their unappealing sweet potatoes cake wins the challenge and with the hostages being rescued, Xros Heart started off a battle. Monzaemon leader then absorbs his Monzaemon followers to become Giga WaruMonzaemon.

Xros Heart find themselves into the Sweets Zone's underground and with the impression that Cutemon's parents are among them, Taiki and others attempt to search for and save everyone only to find themselves surrounded by Raremon. They managed to escape with Nene's Monitamon attack, causing the team to separated into three groups with Zenjirō and Nene learning the Raremon are the prisoners transformed. Furthermore, Cutemon's parents are nowhere to be found as the nearly complete Breakdramon emerges. Shoutmon ×5 is then formed to fight the robotic dragon before Matadormon appears with Cutemon's parents as hostages, forcing Xros Heart to step down with Shoutmon ×5 being attacked nearly to death. However, through his parents' telepathic request, Cutemon heals Shoutmon ×5 as he proceeds to destroy both Breakdramon and Matadormon, with Cutemon's parent being rescued.

Taiki and others comes to Sword Zone, where all Digimon in this zone have a goal to become the real swordsman but Grademon arrives and attack them, causing Xros Heart to fight against him. Shoutmon ×4 who managed to defeat Grademon but Taiki's wishes of hoping all the enemy to become a kind digimon turns Grademon back to itself original form with the Code Crown's power. Grademon later leaves the place. By then, Kiriha appears in front of Taiki and reveals the war for the Digital World is about to commence. Tactimon soon appears and overwhelms Shoutmon ×5 and DeckerGreymon with his Jatetsufūjinmaru and collect the Code Crowns from Taiki's and Kiriha's Xros Loaders to be presented to Bagramon. When Tactimon about to demolish Taiki, Grademon returns and take over his place and lastly sacrifice himself by destroy Tactimon's tower, unlocking and allowing Beelzebumon to enter the Zone.

Ending up back in their world, Taiki, Akari and Zenjirō learn that their time in the Digital World was about half a day in human world time and both of Taiki and Akari's family members have no faith on their words. Taiki later hears the voice who had granted him the Xros Loader, though is unable to find it. The next day, Taiki meet up with Akari and Zenjirō, telling them his intention to go back to the Digital World and save their friends over there. The voice eventually respond to his words leading them to it, revealed to be the DigiMemory of Omegamon. After fully materialising Shoutmon and explaining the origin of the DigiMemories, Omegamon reveals he has the power to return Taiki to the Digital World, but Akari and Zenjirō must stay behind. Just then, Tactimon, who was trapped in the real world and attacking the city, uses the electricity to give himself form and chase over Taiki.

Taiki and Shoutmon return to the Digital World and land in Dragon Land, knowing that through Lilymon (Shoutmon's old village mate) that there are no longer Zones as the Digital World has been reformated into one floating island where Bagramon reigns from, with seven surrounding Lands, each ruled by DarkKnightmon's Death Generals. Taiki and Shoutmon encounter Dracomon, saving him from a mob of dinosaur and dragon Digimon led by Devidramon. Meanwhile, Kiriha arrives and launches an attack at the Bagra Army's Dragon Land branch while calling out the first Death General, Dorbickmon. Answering Kiriha's challenge, having taking out the bulk of Blue Flare with a pit trap, Dorbickmon arrives in his Darkness Mode and uses his Darkness Loader to Forced DigiXros his Flarerizamon into a flaming sword to easily defeat DeckerGreymon. With some help from Lilymon and Dracomon, Taiki manages to get Kiriha away from Dorbickmon's attack.

With OmegaShoutmon trapped, Dorbickmon DigiXros with Fanglongmon to assume his Darkness Mode, and easily reverts OmegaShoutmon to his rookie form. Before Dorbickmon can destroy Taiki and others, Nene shows up and uses a plant-like smokescreen before retrieving the rest out of harm. At her camp, Nene reveals that she and the Monitamon have been disguising themselves as plants to gather information. Meanwhile, Dorbickmon uses the captured Xros Heart member as a bait to force Taki to reveal himself. The next day, Taiki shows up in front of Dorbickmon. However, he acts as a distraction, allowing Dracomon to flood the area while Shoutmon saves their allies. Infuriated, Dorbickmon DigiXros all his minions to become the winged giant Dorbickmon. Safely placing the allies into his Xros Loader, Taiki forms Shoutmon ×5B to fight Dorbickmon but was defeated by Dorbickmon's power. Dorbickmon then grabs Dracomon and attempts to crush him but is stopped by Kiriha, who arrives with MetalGreymon.

With Dorbickmon defeated, Taiki and the rest end up on another Land where they managed to free a Lopmon who being chased by three LadyDevimon. Later, Lopmon reveals that the place where they are now is Vampire Land and that many of his kind have been captured to the Land's Death General's castle for some reason. Taiki and Nene decide to sneak into the castle disguised as Lady Devimon, and Cutemon disguised as a Lopmon, to take out the castle's barrier. Found out, things go from bad to worst when Taiki encounters NeoVamdemon (Bagramon's second Death General) as Lopmon manages to destroy the barrier, with Shoutmon ×5 unable to fight the stronger Death General. The battle then took over by Kiriha yet the unharmed NeoVamdemon then uses his Darkness Loader to Forced DigiXros with his Devimon and LadyDevimon armies to assume Darkness Mode before executing another DigiXros with MetalGreymon, leaving everyone, especially Kiriha, an unexpected shock.

As Xros Heart find themselves in a pinch, they manage to escape when Lopmon makes himself glow white which spooks NeoVamdemon. Lopmon later reveals that NeoVamdemon's weakness is a legendary white Lopmon. As Kiriha and the rest of Xros Heart hold off NeoVamdemon's forces, Taiki along with Shoutmon and Lopmon head to an underground chamber, trying to search the white Lopmon but only to discover it to be a trap laid out by NeoVamdemon. When Shoutmon hears MetalGreymon's melody still responding, he allows himself to be DigiXrossed by NeoVamdemon, along with Lopmon, both of them try to convince MetalGreymon not to give up. Lopmon then summons all the captive Lopmon to form as white Lopmon which then enables Shoutmon and MetalGreymon to digivolving into OmegaShoutmon and ZeekGreymon. However, they are still in the disadvantages stage until Lopmon sacrifices himself to give Taiki and Kiriha the ability to perform a Double Xros, allowing OmegaShoutmon and ZeekGreymon to become Shoutmon DX.

After destroying NeoVamdemon, Taiki and the rest reach Honey Land. Soon, they discover that Lilamon is under attack by a swarm of Honeybeemon who drain her power. Taiki's group tries to save her, only to be stopped in their tracks by a Digimon named Ignitemon, who weakens the group's Digimon under orders from Zamielmon (Bagramon's third Death General). However, the arrival of a Digimon freedom fighter named Mervamon enables the Xros Heart United Army to escape. Soon, they follow Mervamon back to her shelter and discover more Digimon including Stingmon are stung by Honeybeemon with most of their energy being drained off. Soon, they decided to destroy Zamielmon. Back in Zamielmon's lair, Zamielmon's servant GrandisKuwagamon told Zamielmon that the humans he encountered are the ones who killed Dorbickmon and NeoVamdemon.

After Zamielmon escapes, Xros Heart learns from Ignitemon that the Death General's current size was the result of him consuming the DigiHoney created from the energy stolen from his Digimon victims. With this knowledge, Taiki get an idea that he could defeat Zamielmon if they managed get him restore back to his original size. Then, an invitation of Zamielmon to his Tanemon Floramon playground give Taiki the chance to achieve their goal. While Taiki and Nene go to the playground to stall Zamielmon, Kiriha heads to Zamielmon's lair and destroys all the DigiHoney with Beelzebumon and Ignitemon assisting him. Though the plan worked, the team did not expect Zamielmon's true size to be gigantic as Shoutmon DX is unable to fight against the fast-moving opponent. However, thanks to JetMervamon, Zamielmon is stopped in front of his lair and allowed Shoutmon DX to finish him off.

Having heard from Kiriha that he saw a boy who resembled her younger brother, Nene is eager to search for Yū, only to find him and learn that he has been willingly helping DarkKnightmon the entire time. Yū and Tuwarmon then take their leave when Taiki and the others come to her aid, with Nene chasing after her brother. However, Yū summons Doumon to cast a spell on Nene, giving her the delusion of being back in the human world. Tuwarmon whom about to kill Nene was stopped by Mervamon, who emerged from Nene's Xros Loader. Taiki and Kiriha then discovered Nene's exact location and break the illusion as DarkKnightmon appears with Lilithmon (who later been DigiXros with Blastmon and the Vilemon as Gattai Lilithmon by Yū using his Darkness Loader). A chaotic fight soon follows with Doumon destroyed as Yū DigiXros Tuwarmon onto DarkKnightmon for the latter to become MusouKnightmon. OmegaShoutmon and ZeekGreymon are fight in retaliation and the three Digimons' power causes a big bang.

Xros Heart arrives in the futuristic Kingdom, Cyber Land, where they are attacked by an army of Andromon emerging from a Whamon. However, upon defeating them, the gang realize they are only puppet-replicas. Deciding to stop it at the source, Taiki and his companions enter the Whamon-like spaceship and discover a strange girl kept in a capsule within it. Introducing herself as Ruka, she explains that she captured by the Bagra Army. Despite Dorulumon being reluctant to trust her, Taiki and the others quickly accept her into their group as she leads them out from the spaceship. However, Dorulumon soon gets separated from the others because of chasing over Ruka and encounters Cutemon, who is acting strangely. However, the Cutemon turns out to be the fourth Death General known as Splashmon, who possesses the ability to assume any form. Capturing Dorulumon in his trap, Splashmon reveals that his puppets, Ruka among them, are controlled by creatures created by him, called Drippins.

With Dorulumon captured, Splashmon assumes his captive's form to make members of Xros Hearts Team doubt one another, in order to create more negative energy for Bagramon, causing Kiriha to break from the team. From there, Splashmon captures Nene and assumes her form into tricking Taiki, Shoutmon, and Ballistamon into a death trap. The Death General then assumes Taiki's form to mess with Kiriha, only to see the deception has no effect and forces Splashmon to kill him personally. However, Taiki arrives, revealing that he knew it was Splashmon the entire time and played along while Dorulumon and Nene were freed. Furious that his plan to turn Xros Heart on itself failed, Splashmon DigiXros all his Drippins to assume Darkness Mode before easily defeating MetalGreymon and being unharmed by Shoutmon ×4 and Jet Mervamon's attack. After revealing his true water-tiger form, Splashmon overpowers Omega Shoutmon and Zeek Greymon.

After landing on the Gold Land which contains a wide Golden Sea, Xros Hearts found no traces of the Death General, until a pirate ship rises from underwater, revealing the fifth Death General, Olegmon the Golden Thief. Admiring their tenacity, Olegmon offers Xros Heart to join his crew. However, the team refuses and starts attacking Olegmon, only to give Olegmon the chance to force Shoutmon and majority of the Xros Heart members in becoming his minions by casting a spell on them. Thanks to Ballistamon, Taiki and the remaining members manage to escape. Intent on freeing the others, Ballistamon discloses the secret to break Olegmon's spell. After breaking free from the spell, the enraged Shoutmon manages to digivolve to OmegaShoutmon and battles against Olegmon. However, captured by his crew, Olegmon reveals Ballistamon to be one of his most dangerous servants, forcing Ballistamon to transform back to his original form, DarkVolumon.

After being captured, Ballistamon turned back into his original form, DarkVolumon. Despite Kiriha's intervention with Deckerdramon and MailBirdramon, they and OmegaShoutmon are all sent overboard by Olegmon with Taiki tied up. The next day, after begging Kiriha to have him save Ballistamon, Shoutmon has Kiriha save Nene and Taiki while telling the latter to DigiXros him with DarkVolumon in order to reach him. Though it seemed to fail at first, Ballistamon comes to his senses as Shoutmon frees the other Xros Heart members, Lunamon, Coronamon, and Spadamon from Olegmon's spell. Though forming Shoutmon ×4S to lead the defeat of Olegmon's crew, he is unable to fight the Death General. But in a gamble, Ballistamon Xros Opens from the formation to use his ultimate speaker attack which still contains Olegmon's spell to destroy his former leader. Soon after, Spadamon, Lunamon, and Coronamon join up with Xros Heart.

Xros Heart arrives to Canyon Land where the Earth-god General Gravimon, having learned of his fellow Death Generals' defeat, has ordered all his forces to gather around his fortress. Planning to use his group as a diversion for Xros Heart to take the castle by surprise, a plan that Taiki accepts, Kiriha finally reveals he came to the Digital World to become strong. However, once he and ZeekGreymon manage to storm the castle while using their Blue Flare team to take out the Death General's force, Gravimon reveals that he was a step ahead the entire time. Despite having JetMervamon help the Xros Heart United Army escape, Taiki learns that Kiriha is captured. And, to make things worst, Gravimon uses Kiriha's shady past to turn him into his pawn to defeat Taiki.

Kiriha is tricked by Gravimon into believing that Taiki is the reason he could never achieve his goal to be strong as the boy is consumed by the darkness in his heart. Tension runs high as a fight breaks out among the Xros Heart United Army with Taiki being hesitant fight back against Kiriha. Although the core Digimon from both sides were injured badly, Kiriha refuses to stop fighting until Deckerdramon stops it and reasons with Kiriha to regain the love that has lost from his heart. The action failed, and caused Kiriha to have Deckerdramon mortally wound for insubordination. Taiki intervenes so Deckerdramon revealed the rest of Kiriha's past. Later, as Kiriha started to understand the source of his love, Gravimon appears to launch an attack from above with Deckerdramon shielding everyone with his own body. Kiriha soon realized that his power lays within the love and bond between him and his teammates.

Fueled by Deckerdramon's death, the restored bond between Kiriha with Taiki and Nene creates Shoutmon ×7. Although Shoutmon ×7 manages to destroy Gravimon, it is soon revealed, that Gravimon can regenerate himself if his heart is kept safe, by Hi-Vision Monitamon after he sneaks into the castle to investigate before being captured. As Taiki DigiXros Cutemon with Dondokomon, Knightmon, PawnChessmons, Persiamon, ChibiKamemon and Jijimon to form G-Cutemon to hold off Gravimon's army, Nene and Kiriha sneak into the Death General's castle to free the captured Hi-Vision Monitamon and find Gravimon's heart. However, Gravimon expected them to pull off such a plan and DigiXros his remaining forces to assume Darkness Mode while revealing that he secretly transferred his heart into Taiki's left arm during the first battle. Agreeing to Gravimon's demands, Kiriha gives up his Xros Loader in order to save Taiki's life.

Taiki and others arrive in the last Kingdom in the Digital World, Bright Land. They start heading towards the country's tower but Sparrowmon informs that some force field has prevents them to entering it from the sky. On their way, they encounter and attempt to help the country's digimon that was pinned down to the ground by big spikes but was told that only Apollomon (the last Death General) can remove them. Suddenly, Apollomon's army appears, commencing a battle. Learns from the Xros Heart's strenght, the Death General grants them an audience with him on the tower's garden. Instead setting off a fight, Apollomon offers himself to assist the Xros Heart into defeating Bagramon, stopping the ultimate day of destruction 'D5'. Though Taiki believes they can trust Apollomon, it took the Digimon to save the boy's life to convince Kiriha and Nene.

Taiki ends up facing Yuu in a sword fight and is losing against him. By then, the Whispered appears and reports of Kiriha's defeat along with DarkKnightmon and Lilithmon chasing Nene, Shoutmon ×5, Beelzemon and Mervamon. Yuu then reveals how he got to the Digital World and his encountering with DarkKnightmon, making the boy to unfold his true nature. Realizing the truth behind the facade, Taiki picks himself up and defeats Yuu while convincing that what DarkKnightmon said was nothing but lies. But, even with Nene attempt to further convince, Yuu refuses to believe and instead DigiXros DeadlyAxemon, all of Apollomon's minions and Hell's fields' evil energy into Tuwarmon, assuming Deadly Tuwarmon Hell Mode. However, as the Xros Heart members gathered to form Shoutmon ×7 and cause some damages on Tuwarmon, Yuu begins to self doubt his faith in DarkKnightmon. Badly injured, Tuwarmon along with Yuu is forced to withdraw from the battle, who then asking him if Taiki is telling the truth.

Taiki ends up facing Yuu in a sword fight and is losing against him. By then, Whispered appears and reports of Kiriha's defeat along with DarkKnightmon and Lilithmon chasing Nene, Shoutmon ×5, Beelzebumon and Mervamon. Yuu then reveals how he got to the Digital World and his encountering with DarkKnightmon, making the boy to unfold his true nature. Realizing the truth behind the facade, Taiki picks himself up and defeats Yuu while convincing that what DarkKnightmon said was nothing but lies. But, even with Nene's attempt to further convince him, Yuu refuses to believe and instead DigiXros DeadlyAxemon, all of Apollomon's minions and Hell's fields' evil energy into Tuwarmon, assuming Deadly Tuwarmon Hell Mode. However, as the Xros Heart members gathered to form Shoutmon ×7 and cause some damages on Tuwarmon, Yuu begins to self doubt his faith in DarkKnightmon. Badly injured, Tuwarmon along with Yuu is forced to withdraw from the battle, who then asks him if Taiki is telling the truth.

SkullKnightmon along with Yuu escaped from Hell's Field and headed back to the Great Demonic Palace, while Taiki and the others safely reached the Bright Land's surface. Wisemon soon managed to analyze that Apollomon is still conscious despite Whispered being in control. As Kiriha and Nene hold off Apollomon's army, Taiki and his Digimon make their way to Apollomon's shrine. But, as they reach the top, Whispered posed as Apollomon in an attempt to kill Taiki while his guard is down. However, seeing though the deception, Taiki uses OmegaShoutmon to strike the Death General as Kiriha and Nene arrive to form Shoutmon ×7 and the epic battle with Whispered begins. However, after sealing Shoutmon ×7, Whispered starts to collect energy to execute an attack that would destroy all of Bright Land. Though Dracomon and Mervamon free him, Shoutmon ×7 unable to hold the attack off.

After the defeat of all Death Generals, Taiki and the others head to the Bagra Army's Headquarters, Pandemonia. Having been expecting them, the Bagramon turns out to be an illusion with DarkKnightmon dealing with them. DarkKnightmon then reveals the Darkness Stone, the Code Crown that had been infused with the negative energy collected by the Death Generals. He then uses it to revive the soulless Death Generals. As Shoutmon ×7 is formed to hold the monsters off, DarkKnightmon DigiXros them into GrandGeneramon, a destructive beast that cancel off Shoutmon's DigiXros. Later, DarkKnightmon utilize the Darkness Stone to rip off Shoutmon's soul, his DigiCore, before attempting on Taiki's with Dorulumon and Ballistamon sacrificing themselves to prevent it. However, Taiki soon willing let DarkKnightmon to has his soul removed.

In Prison Land, the Death Generals defeated Shoutmon ×3 so easily, but moved by this act of self-sacrifice, Olegmon switch sides to support Taiki against his former teammates, while Apollomon is separated from Whispered to settle their very own battle. At that time, having no intention of keeping his word to Taiki to spare the others, DarkKnightmon has GrandGeneramon to defeat Kiriha and Nene. Later, Apollomon sacrifice himself to help Taiki and his Digimon along with Olegmon in restoring themselves. However, Olegmon died again in the process when the Xros Heart team destroyed the incomplete GrandGeneramon. With their fight against the Death Generals truly over, Taiki and the others head to the actual Pandemonia to face Bagramon and DarkKnightmon while rescuing Yū.

In the Pandemonia, Yū is captured and his power is collected, while Taiki and others finally meet Bagramon and DarkKnightmon outside the palace. Bagramon, who has absorb the Dark Stone, appears before the Xros Heart and reveal the meaning behind D5. Using Jatetsufūjinmaru (Tactimon's sword, that fell into the ocean after his battle with OmegaShoutmon.) as a homing beacon, Bagramon opens a rift into the human world and freeze everything in the vicinity of his extended arm as all energy is drained with Akari and Zenjirō are saved by a mysterious voice. In midst of chaos, Taiki and Mervamon fall into the underground. Meanwhile, Kiriha has OmegaShoutmon and ZeekGreymon to battle against Bagramon. Taking advantage of the distraction, DarkKnightmon stabs Bagramon from the back and proceeds to forced DigiXros, absorbing his brother's power.

After DarkKnightmon absorbed his brother Bagramon in a DigiXros, he reveals that he unsealed the Darkness Loader and used the Amano siblings in order to eventually overthrow Bagramon and become the new ruler of the Digital World. Meanwhile, Taiki managed to rescue Yū from the enlarged Tyutyumon, who was devoured by Bastemon. Taiki then rejoin the rest and brings Yū back to Nene. DarkKnightmon's new form is then confronted by Shoutmon ×7. However, after metaphysically destroying DarkKnightmon, Bagramon takes control of his brother's body and reconfigures it into DarknessBagramon, who then deletes his surroundings and heads into the human world where everything is turned to stone. In the process, he kills Shoutmon and sends the others into a void. Once being trapped there, Taiki and the others were saved by Akari and Zenjirō, who were transported by the power of two DigiMemories (WarGreymon and Examon) that come to life, proposing a way to bring Shoutmon back and save both worlds.

Taiki and the rest are transported back to Earth by the DigiMemories of Examon and WarGreymon. Examon proceeds to reveal Bagramon's plan and the forming of DigiMemories. Soon, Yū's Darkness Loader transformed into a yellow Xros Loader as Examon and WarGreymon's DigiMemories revive Omegamon's DigiMemory. Soon, a decisive battle between Xros Heart United Army and the Bagra Army started. Meanwhile, Taiki, Akari and Cutemon enters into DarknessBagramon's body with intention to search for Shoutmon. As they encountering a metaphysical Bagramon with Taiki nearly killed, the Dark Stone purified into Code Crown and brings every digimon including Shoutmon back to life. The Code Crown then sends Taiki and his team members out of DarknessBagramon's body. Guided by the Code Crown, the Xros Heart executes a DigiXros called Final Xros on Shoutmon with all Digimon to form Shoutmon ×7 Superior Mode. Finally, DarknessBagramon is destroyed for good and everything back to normal.