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.

The Xros Heart boys join the school's kendo club for the regional tournament and after winning a match, they find that they are being observed by Musashi Kenzaki, a student from a rival school. Later, Musashi ends up in the DigiQuartz and meets Kotemon who takes him as his pupil. Some time later, a mysterious figure starts challenging members from adult kendo clubs throughout the city and beats them to the point of shredding up their clothes. Tagiru and the others figure out that this incident could be Digimon related and investigate by themselves until they find that the mysterious attacker is actually Musashi. Tagiru challenges Musashi for a match and he sees a second blade appearing on his other hand for an instant to block his attack. Musashi flees and Kotemon appears, offering himself to train Tagiru asking him to help bring Musashi to stop following the dark path he is taking.

Tagiru, Yū and Taiki go to an okonomiyaki store after school. But the moment the three of them open the door, they go into the world where Digimon live in DigiQuartz, and encounter a Digimon named Pagumon, who loves Okinomiyaki. Tagiru wants to hunt Pagumon. The next day, Tagiru and the others heard about whoever ate the potato chips have either disappeared or flowing in the air. Then Pagumon says "It must be Jagamon's doing!" Tagiru wants to hunt Jagamon so he goes towards the closest convenient store. He stunks looking at the boys and girls who are holding the Potato Chips and flowing in the air, Tagiru goes into DigiQuartz, and plans to hunt Jagamon. However as Tagiru reloads Gumdramon, Pagumon starts to battle themselves. Jagamon notices Pagumon, he sends Gumdramon flying and runs away. They thought that they could find Jagamon, but due to Pagumon's "bad advices", they continue to lose the hunt.

While Tagiru is hunting Zenimon, he has discovered that a mysterious teen named Hideaki Mashimo suddenly appears with a blue-eyed Dobermon and is blocking his way at the Shopping District. Zenimon is a Digimon who likes money a lot and whenever it sits on an ATM machine, the machine will not function properly. In order to overcome this abnormal situation in the street, Hideaki is hunting the Zenimon to get a reward from the shop owner. His main objective is to earn money rather than hunting down the Digimon. His dream is own a takoyaki shop and he is hunting Digimon to save up the money at the same time. Digimon hunting solo is dangerous and he decides to team up with Tagiru, promising that he will share the reward with him. Surprisingly, Tagiru, Hideaki, Dobermon and Gumdramon have encountered a new Digimon named Ganemon. Ganemon is Zenimon's boss and he is trying to capture back the Zenimon, and Ko-Zenimon (a smaller form of Zenimon), who have escaped from his briefcase.

Akari returns to town to visit Taiki, oblivious to the Digimon Hunts. SuperStarmon decides to capture Taiki and add him to his collection of imprisoned celebrity dolls. He lures Taiki and Akari to a deluxe hotel where he traps them in the DigiQuartz. Tagiru, Yū and Ryouma join forces to save Taiki and Akari, and capture SuperStarmon. Yū and Tsuwamon successfully save Taiki and Akari, the latter suggesting Taiki and Yū DoubleXros Shoutmon, Ballistamon, Dorulumon and Starmon and the Pickmons into Shoutmon X4. Shoutmon X4 defeats SuperStarmon and he is captured by Yū. Akari offers her assistance to Taiki when she is available, and Zenjiro bursts into Taiki's room demanding to know where the Clockmaker is. After the fight, Ryouma tells the Clock Owner about what just happened in DigiQuartz.

Tagiru, Taiki and Yū are taken by a Trailmon to an unknown location in DigiQuartz at the request of "a certain person" who needs to meet them. The trio Timeshifts back to the Human World and find themselves in Hong Kong. Yū guides the others around the city until they are picked up by a limo owned by the boy's older sister and fellow Xros Heart member Nene, now a well known idol. Revealing herself to be the one who sent the Trailmon to them, Nene explains that she is being stalked by a mysterious masked man with strange powers and suspects that a Digimon is behind this incident. Tagiru is the most enthusiastic to help Nene, but ends up causing more trouble by attacking and injuring a stage actor after mistaking him for the masked stalker and is forced to fill in. Just then Nene is about to shake Tagiru's hand after a job well done, when the masked man appears and attacks him.

Usually active and passionate students and teachers in Tagiru's school have become lifeless and short of energy. Tagiru suspects that a Digimon is behind this and investigates the DigiQuartz with Gumdramon. Upon investigation, he finds that FlaWizardmon is the one responsible. FlameWizardmon has been absorbing life energy from people to power himself up. Tagiru's passionate energy ends up being absorbed by FlaWizardmon and he himself becomes lifeless. Taiki and Yū find out and investigate the DigiQuartz themselves. Gumdramon stays behind to support Tagiru and eventually carries him to where Taiki and Yū are battling FlaWizardmon. Tagiru finally gains enough passionate energy back and gives his fiery passion of spirit to Gumdramon, Super Evolving him into Arresterdramon. FlaWizardmon is finally defeated and the students and teachers get their energy back.

Masaru Katsuji, a boy in Tagiru's class, seems to be down lately since his family's Ramen restaurant has been getting less customers since the opening of a nearby popular Ramen restaurant opposite them. Tagiru says he will help "Katsuji" to reclaim its popularity, and he and Yū challenge each other to come up with a solution. Later that night, while trying to find a way to improve his ramen, Mr Katsuji gets sucked absorbed into DigiQuartz by the Digimon duo of Ogremon and Fugamon. Though they own a Ramen Restaurant of their own in DigiQuartz with their special hand-pounded noodles, the two oni Digimon offer to give some to Katsuji in return for his delicious soup so both restaurants can flourish. Feeling something is off when the sudden number of customers at Katsuji, Xros Heart learns of Katsuji's deal with Ogremon and Fugamon.

Kiichi who's in the same grade as Tagiru, shows everyone the his pictures of visiting different places around the world. Though their classmates are half in doubt about it, Tagiru learns later that night that Kiichi is traveling via a Locomon. Kiichi invites Tagiru to ride on Locomon, and travel around the world together along with a bunch of other kids from their school. A few days after, the students begin to doze off as Kiichi admits to Tagiru that they been using Locomon to travel on a night basis. Deciding to put a stop to it for Kiichi's own good, Tagiru, Taiki and Yū board Locomon. However, Locomon is derailed by Ren on his Pteranomon before being added to the Digimon Hunter's collection. Kiichi asks Tagiru to bring him along, and get Locomon back with him, while Gumdramon beats Airu's Parasimon and the Hunters escape. In the end, Kiichi and Locomon promise to regulate their trips with the children and their time to sleep, and become allies for Tagiru and Gumdramon.

Tagiru is excited about his success at being a Digimon Hunter before the mysterious clock shop owner gives him an invitation to a contest to determine the strongest Hunter. The invitation reveals a bar code which Wisemon read to discover the location of the contest, a distant island. Tagiru, Taiki, Yū and Hideaki all travel to the island where other Hunters are gathered, learning the objective is to capture a powerful Digimon named Volcadramon. However, Volcadramon proved to be too powerful, scaring off Haruki, Noburo, and Ken and overpowering Tagiru and his friends until Kiriha suddenly appears and captures the Digimon. Kiriha leaves Taiki a warning as Taiki speculates the Clock Shop owner's plan. Meanwhile, the old man comments about the hunters to some very familiar guests...

On his way to school, Tagiru meets a transfer student named Makoto Tamura who somehow has the ability to make everyone he looks at become his friends. With Yuu also affected, Tagiru and Taiki suspect a Digimon to be behind it. However, when they attempt to reach DigiQuartz, the two boys, Gumdramon, and Shoutmon find the schoolyard in DigiQuartz blocked. As it turned out, Makoto's ability to make friends was arranged by Phelesmon in the guise of an angel, who intends to perform a "Sacred Ritual of Friendship".

Fireballs are appearing at telephone box which is located in front of the ruins. Furthermore a strange and freaky voice "H~E~L~P M~E" can be heard through telephone receiver. Learning of this rumor, both Tagiru and Yuu are suspected that a Digimon is behind it and resolve to catch it. When they reached the destination, meeting a teen named Kaoru calls him a "Supernatural Hunter" and intends to solve the "supernatural incident" with science fact. Finding the identified the telephone box and compare it with the uploaded video, they notice that the fireballs, disappear in a rundown drive-in. While exploring the Drive-in, the three end up in a cave and find portable gaming device that is the source of voice. Ending up in DigiQuartz, it is revealed that the voice is actually a Patamon who is being pursued by Airu.

Betsumon is a thief who uses cosplay costumes to resemble other Digimon, making him wanted in the Digital World regardless of his appearance. Wanting to capture Betsumon, Tagiru joins up with the Digimon Hunters who also have business with Betsumon. However, it turns out that Betsumon is an old friend of Gumdramon's though the Digimon does not remember him and goes on the offensive.

Various cryptids have been sighted in town. Tagiru and Gumdramon discover that Ekakimon has bonded with a lonely boy and has brought his drawings to life.

While out fishing, Xros Heart meets a female Digimon Hunter Mizuki and her partner Submarimon. Explaining her story, Mizuki is treasure hunter who heard of a treasure within sunken ship under Tokyo's waters. However, to defend the beautiful sea, and to obtain riches, she became a Digimon Hunter to deal with Dragomon (who is also pursuing a Plesiomon). Asking for Tagiru's help, Mizuki leads Xros Heart to Dragomon's location as he is also searching for something valuable. Tagiru helps to capture Dragomon while Mizuki manages to capture Plesiomon.

Kids across town have been brainwashed by a recent card game. Taiki, Yu, and Tagiru discover that RookChessmon is behind this.

Learning of a Digimon-themed amusement park, Tagiru and Gumdramon follow a pair of Bakomon into the DigiQuartz where the Digimon Land is located. There, confronting the manager Jokermon, Tagiru and company learn that the park is a front for its owner, Sakkakumon, to swallow the energy produced from children's happiness, becoming larger and more powerful for each child he consumes in conjunction to Digimon Land's mutual expansion. Unable to land a hit due to Sakkakumon's ability to absorb enemy attacks and reflect them back three times stronger, Xros Heart is forced to fall back as Jokermon intervenes and orders the Bakomons to capture the three Digimon Hunters. However, the brown Bakomon intervenes with the fight and seals Sakkakumon's openings on his body, causing Sakkakumon's power to fade as a result. Taking advantage of the situation, OmegaShoutmon, Tsuwamon and Arresterdramon defeat Sakkakumon before both Jokermon and him are captured by Tagiru.

Wanting to find out the full story behind the Digimon Hunt, Xros Heart finds a lead in a mythical Digimon named MetallifeKuwagamon. Tagiru's insect-collecting classmate Kaneda enters DigiQuartz with Tagiru and Hideaki. Later on, to Kaneda's dismay, the bug he caught is actually MetallifeKuwagamon who later on takes the boy as a hostage to cover his escape. Eventually, Tagiru and the others find MetallifeKuwagamon with Arresterdramon defeating him while Tagiru saves Kaneda. However, Tagiru realizes MetallifeKuwagamon cannot be captured as the Digimon reveals that his data belongs to an evil Digimon Hunter. Suddenly, before he can reveals his master's identity, an evil being with red eyes and mouth deletes MetallifeKuwagamon before attempting to suck the Digimon Hunters into it. But at the very last minute, Taichi Yagami (who arrives with WarGreymon) and Masaru Daimon (who arrives with ShineGreymon) arrive to the Hunters' aid.

What seemed to be a normal day for Tagiru goes awry when his school is being absorbed into DigiQuartz before finding a Tsumemon that Digivolves into Keramon. When Ryoma arrives, Keramon Super Evolves to Chrysalimon as Arresterdramon and Astamon respectively Xros Up with Ogremon and Triceramon. However, Chrysalimon spreads DigiQuartz to Tagiru's house, making his mom and dad disappear among with other people. Hearing from Ryoma that the rest of the world would follow if this continues, revealing how he got caught up with Digimon, Taiki's group and Ryoma's group join forces to free the kidnapped victims and join the others as they demand answers from a non compliant Old Clock Store Owner. By that time, Chrysalimon Super Evolved to Infermon and overpowering the Hunters' Digimon until Tagiru and Ryoma execute a Double Xros between Arresterdramon and Astamon.

The Old Clock Store Owner explains that to defeat Quartzmon one of the Digimon Hunters must prove him/herself stronger than all the others to obtain the Brave Snatcher, what remained of Bagramon, and infuse it with the powers of Taiki and the five Legendary Heroes from other time-space universes who saved their respective Digital Worlds. Before sending Tagiru, Ryouma and Noboru's teams, and a few other hunters to a separate dimension, the Old Clock Store Owner gives Akari and Zenjirou their own Xros Loaders so they and the reformed Xros Heart United Army can help keep Quartzmon at bay. Finding themselves fighting an army of Myotismon clones which emerged from Quartzmon, Xros Heart forms Shoutmon DX, XrosUpBallistamon with Deputymon, XrosUpDorulumon with PawnChessmon, XrosUpTsuwamon with SuperStarmon and XrosUpMervamon with Beelzemon. The fight takes turn for the worse when some of the Myotismon digivolve into MaloMyotismon and a group of VenomMyotismon.

Though it seemed Ryouma had betrayed the Hunters, Astamon reveals to Tagiru he is the embodiment of Quartzmon's Terminal and has been manipulating Ryouma the entire time. Assuming his true form, Quartzmon reveals that he used Ryouma to obtain enough Digimon data to construct his main body before fusing into it and burrowing underground to turn Earth into data to asborb. The Old Clock Store Owner has everyone gather around him to lend the power from their Xros Loaders, while having Clockmon temporaryily freeze time to halt Quartzmon's digitizing of all life on Earth long enough for Tagiru to obtain the Brave Snatcher. Taiki then passes his goggles to Tagiru, asking him to hunt Quartzmon using the combined strength of himself, Tai, Davis, Takato, Takuya and Marcus. While the others are digitized, Tagiru and Arresterdramon proceed to hunt down Quartzmon with the latter assuming Superior Mode and Digi-Xrossing with the Brave Snatcher to destroy Quartzmon at the root.