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. After Taiki fail to use his DigiMemory in the battle, Tactimon captures Akari and Zenjirō, demanding Taiki to hand over the Xros Loader. However, Akari and Zenjirō's passionate emotions give Taiki's Xros Loader a new power, allowing Shoutmon to digivolve into OmegaShoutmon who manages to destroy Tactimon. Taiki returns to the Digital World with Shoutmon, where his presence is noticed by Nene's brother, Yuu, who is seen with DarkKnightmon and says that he wants to battle against Taiki.
In the Sword Zone, the Fusion Fighters defeat the local Bagra Army commander Grademon, winning the final unclaimed Code Crown. With every Code Crown found, the Zones begin reformatting according to the wills of their respective Code Crown's owners, but Christopher shows up to reveal that the real battle is only getting started just as the Code Crowns begin to reunite. Tactimon arrives to claim the prize at this critical moment, but just when it looks like the Fusion Fighters and Blue Flare have managed to fend off this ferocious enemy, Bagramon himself appears to snatch the Code Crowns and cast both sides back to the Human World. With even DarkKnightmon joining the Bagra Army, the future looks grim.
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. With the Raremon restored back to their original forms, Cutemon says goodbye to his parents as he continues with Xros Heart to the next Zone.
Mikey is drawn to the melody of a dying Digimon, Spadamon. After being healed, Spadamon explains that his home, Sweets Zone, has been taken over by the Bagra Army's Matadormon, who is forcing the captured Digimon to make sweets for him. Xros Heart manages to gain access to Matadormon's castle by claiming that Akari is a master patissere, and challenges the Bagra Army's best patissere, WaruMonzaemon, to a baking contest. Meanwhile, Nene and her team rescue the captive Digimon. Xros Heart wins the contest and challenge Matadormon, Spadamon DigiFuseing with Mikey's Digimon to become Shoutmon X4S. However, Matdormon splits the ground open and Xros Heart falls into the underground region of Sweets Zone.
As the Disc Zone collapses, Mikey quickly transfers all the Digimon over to Shinobi Zone. Shoutmon gets some personal training from Ballistamon and Beelzemon in order to prove himself as a strong Digimon, able to become the Digimon King. A Digimon named Tsuwamon appears and informs them that Blastmon is about to attack before leaving. When Blastmon arrives, Shoutmon ×4B battles him before DigiFuseing with Sparrowmon to become Shoutmon X5B, who destroys Blastmon's body and gains his 22 Code Crowns.
After Nene temporarily travels elsewhere, Xros Heart arrives in the Disc Zone where Kiriha's Blue Flare and Blastmon's armies are fighting. Kiriha has just come into possession of the Zone's Code Crown, and Blastmon challenges him for his collection. However, as the two armies fight they cause the Disc Zone to break apart, and MailBirdramon, Greymon, Shoutmon, and Blastmon fall into the abyss. While Mikey tries to figure out how to rescue them, Kiriha refuses to repair the Zone and help his Digimon, saying he doesn't need weak digimon.
Wanting to impress Nene, Zenjirou offers to sneak into the captured castle, taking Dorulumon, a trio of red Monitamon with him while Mikey and the others cause a distraction in the village. As Zenjirou gets further into the base, he and the three Monitamon become discouraged due to set backs they face. However when Zenjirou notices the desperate situation that Mikey and others are facing, he becomes more determined to succeed with the mission. With a strengthened resolve, he inspires the Monitamon and impresses Dorulumon who in turn holds off the guards while Zenjirou and the Monitamon sneak in to save the princess.
Now in the Shinobi Zone, Xros Heart is immediately met by Monitamon who inform them that the Bagra Army has taken hold of the castle and holds the princess hostage. Nene is insistent on helping them and Akari takes notice, wishing to befriend the withdrawn girl. Everyone then sets out to find the Code Crown of the zone hoping to collect it and then force the Bagra Army to withdraw. On the way, the elder Monitamon informs Mikey and the others that in order to get the Code Crown, they have to make the Code Crown's guardian, Karatenmon, laugh.
After Nene attempts to Zone Transfer but faints instead, the Monitamon give Xros Heart the data to take the whole group back to Monitamon's home Zone to help her recover. However, the transfer is interrupted by Lilithmon's servant Arkadimon, who separates Mikey from the others and casts him into the abyss. Fortunately, Mikey is rescued by the researcher Wisemon, who begins to explain the history of the Digital World, but decides to experiment on Mikey rather than let him rescue his friends. In the end, Mikey convinces Wisemon to help him fight Arkadimon, and they all arrive safely in the Shinobi Zone.
On the run from DarkKnightmon and a brainwashed Kiriha, Mikey and Xros Heart encounter Sparrowmon, who begs for their help to free Nene. He then tells that the Darkness Loader is what DarkKnightmon is trying to revive by gathering up darkness. Mikey and the others then decide they must rescue Nene as well as her brother whom DarkKnightmon is using as leverage for cooperation from Nene. But Lilithmon and DarkKnightmon form a temporary alliance to destroy the meddlesome Xros Heart.
Following the clue Nene left them, Xros Heart heads for the Dust Zone when Mikey is suddenly separated from the rest of the team by a wave of darkness that takes him to DarkKnightmon. Not long after, his X Loader is stolen by a group digimon and the gang soon learns about the tyrant digimon, GranLocomon who rules the zone in a form of tyranny. It seems that he has been searching for the X Loader for a while, and Mikey and crew must get it back before it falls into his hands.
DarkKnightmon and Nene have made their way into the Guardian of the Forest Zone's dwelling after Stingmon was saved by a mysterious light and dragged through the glowing doors. Xros Heart tries to get in but are met with a barrier that Lilamon tells them they can only enter by showing Deckerdramon a display of love and devotion through the legendary "Love Love Dance". Akari and Zenjirou are the ones who have to do the dance as a couple but refuse out of embarrassment, insisting they are not a couple. Will they be able to break into the barrier to save Nene and protect Stingmon and Deckerdramon!? Meanwhile Tactimon has Bagramon take the seal off his sword and Mikey tries to get Kiriha and Sparrowmon to join their rescue mission.
Mikey and others arrive in the Forest Zone, where strong Digimon live. However, they arrive in midair in the sky before falling toward the ground. As they plummet, Beelzemon goes to save Akari and Zenjiro who are falling at a fast rate. In result, the team gets separated: Beelzemon, Cutemon, Akari and Zenjiro as one group while Mikey and Shoutmon are with everyone else. Once safe on the ground, Mikey sends out a search party for the lost Akari and Zenjiro. While separated, Akari and Zenjiro encounter the protector of the forest, Stingmon and his love Lilamon who is convinced the two humans are a loving couple. Meanwhile Kiriha and Nene make their appearances in the zone while Mikey and his group of digimon run into Tactimon!
Lucemon absorbs the power of darkness and transformers into a gruesome and powerful form. Within the giant sphere of darkness he holds is the captured Nene. Mikey tries to rescue Nene but fails and Sparrowmon does her best as well to save Nene. When Mikey suggests that they team up, Sparrowmon refuses by saying she will save Nene by herself as no one on the Twilight side will help her. Can they defeat Lucemon even though their powers are divided? Or will the embodiment of darkness destroy them and the zone as well?
The Heaven Zone is far from heavenly, as Xros Heart quickly finds out from a peaceful and just digimon named Lucemon. The police force lead by SlashAngemon rules with a heavy hand, scaring the inhabitants into obedience and peace. However after they are blamed for a crime they did not commit, Mikey and the others oppose the zone's police. Can they prove their innocence? Or will they face the heavy penalty of death?
After Baalmon is fatally wounded by Lilithmon, Mikey is instructed by Pharaohmon to use the Sand Zone's Code Crown which rises a pyramid that carries Xros Heart and Baalmon away from Lilithmon and her SkullScorpiomon army. Mikey uses his DigiFuse 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 Xros Heart all band together to fight while being unable to Digi Xros. Will they be able to fight in their reduced state and can Mikey save Baalmon?
The battle between Blastmon and Nene and Kiriha's forces continue. Meanwhile, as the Fusion Fighters investigate 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 Mikey and the statue to take a tumble deep underground, separating the kindhearted general from his friends. Baalmon then appears before Mikey and says Mikey has been blessed by the goddess and is now her warrior. In response, Baalmon helps lead Mikey from the underground while enlightening him about the past of the Sand Zone and the goddess warriors. Eventually Mikey learns more about Baalmon himself and his tragic past...
Now in the Sand Zone, Xros Heart is suffering from the blazing sun and quickly falls into a sand trap laid by Scorpiomon of the Bagra Army! Then falling deep underground, the team is cornered by a bunch of Scorpiomon just before Revolmon appears and saves them! Only it seems that as a favor for saving them, Xros Heart must help Deputymon with his treasure hunt! But it's not going to be an easy task as what's a treasure hunt without some booby traps and battles!? Not to mention the Bagra general Blastmon is currently present in the zone!
Arriving in the Lake Zone, Xros Heart quickly discovers that the Bagra Army is present thanks to IceDevimon's frozen victims. After rescuing a drowning Knightmon, Mikey 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. Not only that but Mikey's rival Kiriha is at the castle as well!
Tactimon attacks Xros Heart and captures Dorulumon and Mikey, ordering their execution. Meanwhile Nene informs Kiriha of Mikey's capture and he comes to fight Tactimon. While Tactimon is distracted by Mailbirdramon and Kiriha, BlueMeramon helps Mikey and Dorulumon to escape along with the rest of Xros Heart. The group then learns more about Dorulumon's involvement with the Bagra Army while they look for Mikey's X Loader.
