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.

Nene and Kiriha are searching for Yuu while Taiki and Wisemon are working on opening the path that allows them to get back to the surface, without needing to sacrifice either Taiki or Yuu's life. By then, the wounded Beelzebumon and Mervamon set off to find for Yuu, finding the boy before he is captured by SkullKnightmon. As for the badly injured Lilithmon, Whispered DigiXroses her with Blastmon to assume her Demonic Beast Mode while proceeding to negate Hell's Field and erase everything in it. Seeing this monstrous threat, Taiki, Kiriha and Nene quickly form Shoutmon ×7 to prevent both the black and white castles from being destroyed. Informed by Wisemon that both castles are elements crucial to get make their way back to Bright Land, Taiki risks himself to give false death data to unlock the path. Following the success, Taiki faints. As the path opens, SkullKnightmon and Yuu leave the place, followed by the Xros Heart United Army.

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.

It is a year since Taiki Kudō's adventure in the Digital World as he forms the “Xros Heart” basketball team together with Yū Amano, who became his junior at his school, and Tagiru Akashi. However, on his way home from game, Taiki sees a monstrous shadow within a space fluctuation before being confronted by three children. The leader of the trio recognizes Taiki and his potential but tells him not to meddle in their affairs before leaving. The next day after school, Tagiru hears a voice begging to be saved, and after seeing a spacial distortion, Tagiru gets dragged right into it and ends up in a Digital World like dimension called the DigiQuartz, where time flows differently to the real world. Tagiru sees the source of the voice, Gumdramon bring attacked by a MetalTyranomon until the three children arrive and fight it with their Digimon, but it escapes from them. After being told they are Digimon Hunters, Tagiru wants to be one too as he is told to get a X Loader first.

After returning to the Real World, finding out that Digimon can be Reloaded outside of DigiQuartz, Tagiru learns of Taiki and Yū's past experience with the Digimon a year before. Inspired to be at Taiki's level, Tagiru returns to DigiQuartz to begin a new Hunt. The two encounter a mysterious shadow behind the abductions of students: Sagomon. Sagomon overwhelms Gumdramon before he and Tagiru are saved by one of the three children, Ryōma Mogami. As this occurred, going to the alley were Tagiru got his Xros Loader, Taiki meets the Old Clock Store Owner and his Digimon Clockmon. The Owner proceeds to warn Taiki not to interfere with the Hunts due to expertise having an effect that would upset the balance of the "game". Though not intending to take part, Taiki promises to interfere if any one gets hurt in the cross fire. Nothing that Taiki has a strong will like Tagiru, the Old Clockmaker leaves, but not before giving Taiki the Hunter's Rulebook, which Tagiru forgot to get.

The members of the school's robotics club are frustrated because they keep failing to build a robot good enough to take part in the upcoming competition when they approached by Xros Heart's old friend, Puppetmon, who offers them a chance to take part in a greater project. The next day, while told to deliver a notice to the absent Tokio, Tagiru learns from Taiki that all other members of the robotics club are also absent from school, and fearing it to be Digimon related, he and Yū accompany him to Tokio's house, just to find him working on some machinery. Figuring that Tokio is deceiving his mother in thinking he is going to school to stay home, Xros Heart witnesses Tokio entering into the DigiQuartz through his computer. By following him there, they learn that Tokio and the other missing children have been building a GigaBreakdramon under Puppetmon's orders. Taiki and Shoutmon confront Puppetmon who seems to not remember them at all and launches GigaBreakdramon against them.

Tagiru's classmate Miho Sudo has been 1st place Honor Student since Elementary, stresses out on improving her grades when she is at 8th place. Miho's desire for the top 7 students to disappear attracts the attention of a Digimon who offers to make it a reality for her. Later, feeling jealous of Tagiru and Gumdramon, Yū meets Miho. Soon after, news of the two top students in their grade, Mishima and Takahashi, being attacked and looking malnourished drives everyone in school in an uproar. Only Miho had no reaction to the event as Yū follows her while Tagiru enters the Digi Quartz and finds the school covered by a vine looking plant whose tendrils are wrapped around Mishima and Takahashi while draining them. Losing the vines' source, a flustered Tagiru and Gumdramon are encountered by Ren as he tells them that can not defeat vine Digimon unless they find its true form. Deciding to help for his own benefit, Ren has Dracmon bite into the vine to expose the Digimon.

At a cute store called the Fancy Shop Dream, Airu Suzuki, along with her Digimon Opossumon, capture a bunch of other Digimon. Finding that all of them are "no good", Airu leaves the Digimon to her teammates. Still feeling down about not being able to reunite with Damemon, Cutemon appears in front of Yū to cheer him up but ends up being targeted by Airu, who wants to add him to her cute Digimon collection. While Yū returns home, with Tagiru and Gumdramon tagging along, Cutemon spots a bunch of pictures of Nene, who has since become an idol in Hong Kong. After falling asleep from their meal, Cutemon, Tagiru, and Gumdramon awake to find Yū gone. Finding Yū at the park where he and Damemon first met, Tagiru, Gumdramon, and Cutemon make just in time as Airu transports Yū to the DigiQuartz. Trying to force Yū to hand over Cutemon, Airu nearly succeeds, until her DigiXros of Opossumon and Candlemon allows them to escape.