Tagiru, Taiki, and Yuu are invited to an event on a certain island where the strongest and most experienced Digimon Hunters can Hunt a powerful Digimon. When the event starts, they enter the forests in search of the powerful Digimon that lurks there, Volcdramon. Taiki and the others try to Hunt him, but the intense heat he unleashes makes it a difficult battle. Then, someone who didn't enter the event joins in! Who could he be?!

Tagiru's classmate, Kiichi, has begun riding on the locomotive Digimon, Locomon, and traveling to other countries every night. Eventually Kiichi and the other kids who spend all their time traveling with him start coming to school with very sleepy faces. Kiichi also starts to look thin and haggard. Worried, Tagiru and his friends decide to stop Kiichi from going on his trips. They start to board Locomon, but just then something happens! Ren, riding on Pteranomon, captures Locomon. Kiichi is stunned to see Locomon taken away and pleads for his return. Tagiru and company take Kiichi along to follow Locomon. Kiichi tries to persuade Locomon to come back to him. Will they succeed in granting Kiichi's wish and taking Locomon back from Ren?!

Masaru is Tagiru's classmate and the son of the owner of a ramen shop, Katsuji, which has seen a significant decline in customers recently. Determined to help his classmate, Tagiru vows to make Katsuji into the kind of ramen shop that customers will line up to get into. But just when he's about to take action, Katsuji's ramen changes dramatically and people start to form a long line to eat it. Lurking behind this change are the shadows of Digimon called Ogremon and Fugamon! Ogremon and Fugamon have opened a ramen shop in the Digimon world, DigiQuartz, but since business is poor, they approach Katsuji, Masaru's father and the owner of the ramen shop Katsuji. They agree to cooperate using Ogremon and Fugamon's superb noodles with Katsuji's prized soup. Katsuji's shop thrives as a result. However, at the same time, Katsuji's kind temperament changes and he begins to yell at customers. Wanting his kind father back, Masaru decides to make his own ramen to open his father's eyes. What will happen when Tagiru and company stand by his side in this ramen face-off?!

Ninth grader and master swordsman Musashi Kenzaki, who sees Taiki as his rival, begins to undergo kendo training with a Digimon named Kotemon. As this goes on, incidents of rampant test attacks begin to occur! Sensing that a Digimon might be involved, Tagiru sets out on a Digimon Hunt with Gumdramon. They then discover that Musashi is behind the test attacks. Musashi insists that he was fighting fair and square, that they were proper duels and not test attacks, but in the next moment he's surrounded by a black aura...! Is it Kotemon's doing, or is another Digimon behind this...?! Tagiru and company take a stand to find the truth behind Musashi's black aura!

Yuu still hasn't forgotten the pain caused by the loss of his Digimon partner, Damemon. When the Digimon Hunter Airu sees one of Yuu's long-cherished Digimon, Cutemon, her heart is instantly taken! In order to steal Cutemon, she takes Yuu to the Digimon world, DigiQuartz, and traps him. Cutemon tries desperately to save him, but his strength is nowhere near enough... Tagiru and Gumdramon manage to save Yuu and Cutemon once, but of course, Airu has no intention of giving up! She continues to relentlessly pursue Cutemon. Eventually the Digimon Hunters Ryouma and Ren, along with Tagiru, Taiki, Shoutmon, and Dorulumon, also become involved in the heated conflict...!

When Tagiru's classmate Miho Sudo grows jealous of the school's higher-ranked honor students, she ends up possessed by a Digimon! The next day something strange happens to the top two honor students, Mishima and Takahashi, in the middle of class. Their skin suddenly turns brown and they appear to wither, as if something is sucking the nutrients out of them. Sensing that this is a Digimon's doing, Tagiru warps to the Digimon world, DigiQuartz. There he sees strange things that look like plant vines scattered throughout the school and wrapped around Mishima and Takahashi, as if to conceal them. Tagiru and Gumdramon attempt to find out just how far the vines reach. Just then the Digimon Hunter Ren appears and tells Tagiru that the vines themselves are a Digimon, and a very strong one that keeps its true form hidden. When Ren has his Digimon partner Dracmon bite through a vine, Miho, back in the real world, appears to feel intense pain. Then the Digimon that had wrapped itself completely around Miho and assimilated her body, Blossomon, appears! When Miho and Blossomon warp to DigiQuartz, a fierce battle with Tagiru and company begins!!

Students from Tagiru's school are disappearing one after another! Meanwhile, Tagiru and Gumdramon have sensed something moving in the Digimon realm, DigiQuartz. Following its trail, they discover someone, or something, carrying a boy from Tagiru's school... Tagiru rushes to follow him, but then he's attacked by Sagomon, a Digimon that looks like a kappa! As even experienced Digimon Hunters call Sagomon a tough customer, Tagiru and Gumdramon are no match for his fierce attacks... Soon after, Tagiru confronts Sagomon again. He Digivolves Gumdramon in an attempt to capture Sagomon, but they are only pushed back further. When Taiki, who has been watching their struggle, declares "I can't turn my back on them!", Shoutmon hears him and responds. After reloading from Taiki's Xros Loader, Shoutmon Digivolves and gains further power through a DigiXros fusion. He then launches his attack on Sagomon! How will their battle end?!

An email from Pinocchimon appears on the computer used by the robot club at Tagiru's school. Pinocchimon shows Tokio and the other club members a blueprint and some parts and asks them to help him build a robot, luring them to the Digimon world, DigiQuartz. From that day onward, Tokio and the other club members turn up absent from school. As requested by the teacher, Tagiru visits Tokio's house accompanied by Taiki and Yuu. When he sees Tokio working on building a robot as if possessed, Tagiru grows suspicious and decides to observe his movements. Tagiru and the others then watch as Tokio opens an email and enters DigiQuartz through a portal that opens in his computer screen! They rush after him and find themselves in an industrial area in DigiQuartz. They call upon the strengths of their Digimon companions Gumdramon and Shoutmon to locate Tokio and resume the chase. When they follow Tokio into a factory, they find a nearly completely assembled GigaBreakdramon...?! Tagiru and the others try to bring Tokio back from DigiQuartz, but at that moment Pinocchimon appears and starts up GigaBreakdramon. A new battle begins - how will it end?!

A Digimon that steals humans' motivation shows up. The Digimon, called FlaWizarmon, steals Tagiru's motivation, leaving him limp and drained of energy. He's left so listless, he can't even make Gumdramon Digivolve. Meanwhile, FlaWizarmon continues to steal more and more people's motivation. Taiki and Yuu, along with Shoutmon and the other Digimon, attempt to defeat FlaWizarmon and return Tagiru to normal. However, after absorbing Tagiru's motivation, FlaWizarmon keeps getting back up no matter how many times they knock him down...! What is the fate of Gumdramon, who's caught in a major bind without his partner's motivation...? Will Tagiru ever go back to being the super-motivated middle schooler he used to be?!

After receiving an urgent call for help from Nene, who is working as a popular idol in Hong Kong, Tagiru and his friends head to Hong Kong. Nene says she's been having problems for about a week with a stalker in a mask following her around. Worse yet, when the police pursued the masked stalker, he escaped to DigiQuartz, the Digimon world! Tagiru suddenly becomes intent on protecting Nene, but it turns out the masked stalker is a powerful foe who uses Harpymon, a Digimon with extraordinary flying ability, in his schemes! The strength of Nene's Digimon, Sparrowmon, is essential to defeat Harpymon. Nene and Sparrowmon immediately join Tagiru and company as they all venture into battle together!

Taiki meets his childhood friend Akari again, and the two of them find themselves attending a dinner buffet party at a luxury hotel. Tickets for this party are normally rare since the event is booked full all year round, but somehow Akari won the tickets from a supermarket giveaway. But, of course, Yuu is on the scene! It turns out the whole thing was a trap set by the super celebrity star Digimon, SuperStarmon, to catch the superstar Digimon Hunter, Taiki. When Taiki is taken to the Digimon world, DigiQuartz, Tagiru and the others set out to save him. How will their battle end...?!

A great number of Digimon called Zenimon appear in the shopping district, hanging out near cash registers and messing up the machines. Tagiru tries to hunt a Zenimon, but his target is snatched from him by a boy named Hideaki Mashimo. Tagiru and company make an agreement with Hideaki, who is only involved in the Digimon Hunt to make money and has no interest in Digimon at all, to capture Digimon together. As this goes on, Tagiru encounters a Digimon called Ganemon! They learn that the Zenimon are Ganemon's underlings, but something happened and they all escaped. Ganemon asks them to help him recapture the Zenimon, so Tagiru and the others team up with him! However, soon enough something changes in Ganemon, sending the shopping district into a panic?!

Tagiru is on the Hunt for a Digimon that loves the smell of okonomiyaki, called Pagumon. The next day a Digimon called Jagamon, who makes people eating potato chips float in the air and disappear, suddenly turns up. Tagiru reloads Gumdramon to Hunt Jagamon, but they fail because of Pagumon. This causes Tagiru and Gumdramon to argue, and Gumdramon enters the rival Hunter Ryouma's Xros Loader! Tagiru and Gumdramon are thus separated. In the midst of all this, Tagiru watches as something strange happens to Pagumon after chowing down on an okonomiyaki... What will happen to Tagiru and Gumdramon's friendship, and with Pagumon who has fallen into an unforeseen crisis?!

The new chapter in the Digimon Xros Wars series, Time Traveling Hunter Boys, finally begins! The story takes place one year after the battle with the Death Generals. Taiki has started a basketball team, Xros Heart, with his school underclassmen Yuu and Tagiru. Life has been peaceful. Then, one day, the air before Taiki flickers and a monstrous shadow flashes before his eyes. He then meets three mysterious characters - Ryouma, Ren, and Airu - who tell him "This town may become a bit chaotic. Our own game is about to begin." What could these words mean...?! The next day, Tagiru hears the voice of a Digimon on the verge of death, Gumdramon. This leads him to DigiQuartz, a game world inhabited by Digimon. Fascinated by a Digimon Hunt he witnesses there, Tagiru teams up with Gumdramon and starts on his way to becoming a Digimon Hunter!

Takato, Henry and Terriermon have trouble getting out of the strange setting. Takato receives e-mail from Yamaki.

Although Rika and Renamon go to look for their missing friends leaving Kazu and Kenta behind, the boys feel uneasy about being left behind and come after them.