Marcus Damon is a 14 year-old middle school student who suddenly had his life changed the instant he met a lizard-like creature - Agumon. The two actually met in a fight in the middle of the city after Agumon escapes a facility from the organization known as DATS. Yoshino, a member of the organization is dispatched to locate and bring back Raptor 1 (Agumon). She spots Marcus and Agumon who are engaged in a fight. After sometime the two tire out and it appears to be sunset. Suddenly Agumon declares that he will become Marcus' employee because no human has ever matched his strength. Yoshinno calls for Lalamon, her partner digimon, to help capture Agumon. Lalamon performs her Seed Burst attack only to be countered by Agumon's Pepper Breath. The two attacks collide causing a big "smoke bomb" effect to occur allowing Marcus and his employee to escape. Marcus ends up taking Agumon to his home where Agumon claims he is hungry. So Marcus asks him to not move while he gathers some food. Just as Marcus is paying the store clerk for his groceries a girl appears adding in a cup of pudding. She introduces herself as Yoshino from DATS and explains all about their cause and eventually takes Marcus to their heeadquarters where he meets Commander Sampson and his partner digimon Kudamon. Marcus says that he will take responsibility for anything that Agumon does just as an alarm sounds. Marcus runs back to his house only to find that Agumon has disappeared. Yoshi ended up following Marcus as well to his house which is near the site of the Burger stand which was attacked. As Marcus runs out of his building he finds Agumon with his head buried in a trash can of some sort. In reality it was a Kokatorimon who attacked the stand. Agumon and Marcus defend his honor by attacking Kokatorimon. The giant bird is angered and unleashes an attack which knocks out Agumon. Marcus is infuriated and attacks the bird digimon so hard it causes his fist to glow. An old fisherman appears and explains why this is so and tosses a Digivice and tells him to use his DNA to help Agumon wake up and Digivolve. GeoGreymon appears and defeats the Kokatorimon with his attack Mega Flame.

Yoshino drags Marcus and Agumon back to DATS for the return of Agumon back to the Digital World. Marcus keeps trying to plead for Agumon not to be sent back as they watch the PawnChessmon drop the Kokatorimon digi-egg into a machine for transport to the Digital World. As the PawnChessmon begin to drag Agumon into the machine Kamemon waks by with a kettle of boiling water and Marcus kicks it leaving steam all over the place. This gives Marcus and Agumon the chance to escape. As he escapes Marcus drops his digivice. As the two are out of the building Marcus hides Agumon under a box and walks to his home and hides him there. Sarah, Marcus' mom walks into the room while Agumon is clumped up in the closet. When she leaves Agumon comes out but Sarah comes back in and Agumon must hide behind the curtain and out in the Terrace. Kristy, Marcus' sister, finds Agumon and he scurries up to the roof where Marcus chases him and the two fall over and are knocked off the roof. When Marcus awakes in his room he find Agumon and Yoshino eating dinner like family. She tells Marcus that she must keep an eye on the two of them indefinably. She edns up taking Marcus' bed while Marcus himself and Agumon sleep on the floor. In the morning Marcus head off for school but on the way there at Kristy's school there seems to have been an attack since there are dozens of police officers. Before he can get there Yoshino return the digivice and explains how to hide Agumon in it. Kristy explains what happened and Marcus plans a stakeout to catch what could be a rouge digimon. During the night Marcus uses Agumon as bait in the torn cages. Kunemon appears and it seems he is the attacker. Lalamon tries to stop the Kunemon but is no match. As Lalamon lays on the floor Yoshino activates her digivice and use her fist to allow Lalamon to digivolve into Sunflowermon. As that happens Kunemon cocoons itself and digivolves into Flymon. Using it's paralyze attack it stop Yoshi and Sunflowermon. Angered, Marcus punches the digimon in the face and allows Agumon to once more digivolve into GeoGreymon to defeat Flymon. The man who gave Marcus his digivce appears again and explains of all the battles waiting in the digital world. The next morning Marcus and Agumon beg Commander Sampson to join DATS which he accepts dropping the "charges" on Agumon.

Marcus is on his way to town when DATS receives a signal that a DemiMeramon is nearby. DATS notifies Marcus since he is nearest to confront the problem. Once Agumon gets there he and Marcus try to defeat the DemiMeramon but to no avail. Since it is made of fire Agumon's Pepper Breath does no damage, and since it is not dense enough Marcus can not punch it. THe DemiMeramon runs off and the two DATS members chase it off. Elsewhere Thomas is seen working in another country in another division of DATS and announces that he will be going back to the Japan Division. At DATS headquarters Thomas makes his surprising return and shows up with a DemiMeramon egg. Marcus tries to introduce himself but Thomas takes no notice. Seeing how Marcus acts makes Thomas request to Commander Sampson that Marcus be removed from DATS, permanently.

Touma and Masaru are ordered to work together to capture Numemon, but they were unable to do so and resulted in the escape of Numemon before Raramon came to their aid. Suddenly, a Drimogemon appeared and helped two burglars to steal money. Masaru and Touma were ordered to work together again to capture Drimogemon, but they failed again and the digimon escaped to the Digital World. Touma, feeling responsible for the escape, dove into the Digital World against captain Satsuma's orders.

Masaru, Touma, Agumon and Gaomon entered the Digital World to chase after Drimogemon and ended up in a large underground labyrinth. But somehow Masaru came up with a strange idea and they all escaped the labyrinth safely, just to face Digmon (evolved from Drimogemon).

This episode started with Masaru+Agumon fighting against Tortomon. After winning the battle, Agumon became angry at Masaru and hides in his digivice after some rash comments and arguments. Meanwhile, Elecmon is causing chaos in the city. After it evolved into BlackGarurumon, Touma and Gaogamon tried to fight it, but to no avail. Masaru and Agumon came to terms to help Touma and Gaogamon fight BlackGarurumon.

It's Chika (Masaru's sister) birthday and Masaru promised to spend the day with her. The problem is, Masaru has to go to school for some exams to save his grades, so he ended up asking Touma to spend the day with Chika in his place.

Yoshino is dating Neon Hanamura, a famous teen idol who also happens to be her friend since childhood. However, it was all a cover for Yoshino's real work, which was discovering the truth behind Neon's sudden rise to popularity. As it turned out Neon was using a digimon (Kurisarimon) to "hypnotize" people into liking him.

A famous boxer who has been out for a while due to injury (and also Touma's favorite boxer) is back better than ever. His sudden comeback raised some questions and it reeked of a digimon's handiwork. Touma and the team set out to investigate and discovered that it was the work of the boxer's daughter to had a Togemon at her command.

Touma invites Masaru and Chika for lunch at his mansion. After some stupid remarks made by Masaru, Chika bursted out, cursed at Masaru, and stormed out of the mansion. After that, strange things kept happening to Masaru. It turned out that it was the work of Soulmon who turned Chika's words into reality.

The owner of a pastry shop is suddenly addictive to gambling and having a winning streak. After some investigating, Masaru found out that he's been praying in a mysterious shrine with a digimon-like statue, which turned out to be a real digimon - Evilmon. With his henchmen, the DemiDevimon, Evilmon has been doing dirty tricks to help the man win in his gamblings.

A digi-egg found its way to Chika, and Piyomon hatches from it. The two became instant friends. Later, Masaru is told that regular people can't keep digimon as partners unless they're DATS members. This torn Masaru up since he doesn't want Chika to be in danger by becoming a DATS member. Meanwhile, a new digimon - Falcomon appeared in the human world to claim the digi-egg back and found out that it's hatched into Piyomon. Now it wants to bring Piyomon back to the digital world.

Mercurimon appears in the human world to help Falcomon in its battle against Masaru and the others. In the battle, Piyomon's turned back into a digi-egg after trying to protect Chika. Not long after, in the digital world, the digi-egg hatched again and this time, Piyomon evolved into an Aquilamon and went back to the human world. In a desperate attempt to find Chika, Aquilamon further digivolved into Garudamon and wreak havoc across the city. Feeling overwhelmed and frustrated by Garudamon's power, Masaru developed a new power that lets GeoGreymon to evolve into RiseGreymon to finally defeat Garudamon.

To prevent further attacks from digimon, DATS permits Masaru, Touma, and Yoshino to go to the digital world. Upon their arrival, however, they were immediately attacked by a boy named Ikuto who calls himself the digimon warrior and has a deep hatred toward humans.

As the team wander deeper into the digital world, they found a ghost city that nests a horde of Dokugumon. The Dokugumon then trapped the team and brought them into the abyss of the city where their lord MetalPhantomon resides. He casts the humans into a deep world of painful memories. After being shown his deepest nightmare, Touma overcame it and he developed a new power that allows Gaogamon to further evolved into MachGaogamon.

Suddenly Yoshino fell ill, which turned out is caused by a virus that affects humans in the Digital World. While Masaru, Touma and their partners went to look for medicine, Falcomon and Ikuto tried to attack Yoshino and Raramon, but Ikuto was infected by the virus as well. Falcomon ended up asking to join Touma and Masaru in search of the medicine. Meanwhile, Gotsumon sends Blossomon to pursue the team.

Yoshino feels like she's bringing the team down because of her battling abilities. She's not confident since she's the only one whose partner still can't evolve further. Suddenly Gotsumon orders Mammothmon to attack the team. In the middle of the chaos, Raramon stood up to Mammothmon even after Yoshino gave up. This courage of Raramon slapped Yoshino awake and she called forth a new power that allows Raramon to evolve into Lilamon.

Finally the team arrives at the Infinite Ice Ridge to challenge Mercurimon. Surprisingly, the old man that gave Masaru his digivice, Mr. Yushima was also there accompanied by his digimon - Kamemon. Once inside, they were swarmed by Tsumemon and then challenged by Ikuto who swore to defeat all humans in the Digital World. However, Gotsumon turned his back on Ikuto and betrayed him, while capturing the team except Masaru and brought them to Mercurimon's place. After saving Ikuto from death, Masaru and Agumon proceed towards Mercurimon's lair.

As it turns out, the old man Yushima's true identity is that he was the commander of the original Digital World exploration team, as well as DATS chief. Together with the team, Ikuto, and the others returned to the real world after having to leave Yushima behind who "sacrificed" himself to keep digital gate open. After their arrival, Satsuma, the leader of DATS told Masaru and Ikuto about what happened 10 years ago. Meanwhile, Gotsumon broke into the real world with 3 Okuwamon to hurt Ikuto.

The team arrives at Ikuto's parents' house - the Noguchis. However, Ikuto ran away in shock after seeing his real mother. At the Noguchis', Mr. Noguchi explained that his wife went into shock after losing Ikuto 10 years ago and that they were part of the exploration team back then. Meanwhile, while Misuzu, Ikuto's mother was still in the house, Hagurumon broke through the Noguchis' experimental digital gate and took over the house, trapping Misuzu and Ikuto's baby sister in the process.