It is a year since Taiki Kudō's (Mikey Kudo in english) adventure in the Digital World as he forms the "Xros Heart" (Fusion Fighters) basketball team together with Yū Amano (Ewan Amano), who became his junior at his school, and Tagiru Akashi, the new main character. However, on his way home from the game, Taiki sees a monstrous shadow within a space fluctuation before being confronted by three children.

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.

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...

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.

At a cute store called the Fancy Shop Dream, Airu Suzaki, 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.

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, 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.

Soon learning that a new hunter named Hideaki with his partner Dobermon, uses Digimon hunting to earn profit, Tagiru and Gumdramon hunt Zenimon around the Shinonome Higashi Shopping District. Although while in Digi-Quartz, they stumble upon a Ganemon, who is searching for the Zenimon he said to be "lost".

Akari (Angie) 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.

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.

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.

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 and absorbed into DigiQuartz by the Digimon duo of Ogremon and Fugamon.

Kiichi who's in the same grade as Tagiru, shows everyone 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.

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.

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.

Near an abandoned hospital as the rumors have gone around, a mysterious phone booth is a clue to a mystery. Tagiru and Yuu along with their Digimon partners go to investigate only to meet a Spirit hunter named Kaoru. Following her to an abandoned power plant to seek out answers. While they are there they run into Airu, who set traps inside. She states that her Opposumon was taken control by a ghost. As Kaoru mysteriously vanishes in thin air the Hunters don't know what's ahead of them...

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 a 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).

Kids across town have had their rare cards stolen by a mysterious masked person. Taiki, Yu, and Tagiru discover that RookChessmon is behind this. By using a child's greed for more rare cards, he feeds upon it making him stronger and making the masked person get his wants.

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.

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.

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 Evolves into 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.

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.

Though it seemed Ryoma had betrayed the Hunters, Astamon reveals to Tagiru he is actually Quartzmon's Terminal and has been manipulating Ryouma the entire time. Once slide-evolving into 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 digitize the Earth for asborbing.