Kazu and Kenta stray into the house of a Jijimon and a Babamon along with Rika and Renamon and they dream of becoming Tamers.

Takato secretly sneaks Guilmon into his house and, in the meantime, Rika, a digimon tamer, and her digimon, Renamon, easily defeat a Goblimon. Takato leaves Guilmon alone while he goes to school, but Guilmon follows him and causes chaos in the school. Takato meets Henry and his digimon Terriermon and thinks he isn't worthy of having Guilmon. While looking for a place for Guilmon to stay, Takato and Guilmon are attacked by Renamon and Rika.

After the battle with Devidramon, Takato tries to make Growlmon de-digivolve into Guilmon, but all to no avail. When it begins to rain, Takato despairs of ever getting his old friend back. However, when the rain ends, Growlmon de-digivolves into Guilmon while watching the rainbow.

The second group falls into a strange dimension full of clocks. After being attacked by a Megadramon, the group meets Ryo, the legendary tamer who once beat Rika in a tournament.

The group meets an Andromon who is trying to defeat an Orochimon in order to free his Gekomon slaves. Andromon after losing too much energy de-digivolves to Guardromon and Orochimon kidnaps Jeri to have her serve milkshakes to him forever. Kazu befriends Guardromon and saves him by having the Gekomon use milkshakes to heal him and the two come up with a rescue plan. The group manages to reach Orochimon without trouble, but he's too strong for Guilmon, Renamon, Leomon and Guardromon. Thanks to some encouragement from Rika, Jeri does her first ever Digi-Modify and as a result Leomon is able to destroy Orochimon. Thanks to his new friendship with Guardromon, Kazu becomes a Tamer with Guardromon as his Digimon partner, shocking everyone.

Henry and Terriermon stop the fight between Guilmon and Renamon, and Takato finds a perfect hiding place for Guilmon while he’s away. Guilmon and Renamon resume their fight, and Terriermon gets in the way of an attack. He digivolves into Gargomon but can’t control his powers and almost hurts Rika but she is saved by Guilmon.

Rika is disappointed with her mother and with Renamon for not being able to digivolve while fighting Allomon and instead getting help from Guilmon and Terriermon. Renamon goes by herself and meets Impmon, who tells her she doesn’t need a human to make her stronger. When a Dokugumon appears and Renamon is badly hurt. Rika cares for her and she digivolves to Kyubimon and easily defeats Dokugumon with one hit. Kyubimon explains that what finally caused her to digivolve was Rika caring for her.

During a school camping trip Takato, Henry, Guilmon, Terriermon and Calumon have a fun time relaxing. Even Impmon joins in and has fun. Soon, a series of black outs cause the gang to get suspicious. It turns out a Rooster Deva Sinduramon is absorbing electricity and using it for power. The Sinduramon heads for the dam for more power but proves no match for Gargomon and Growlmon and is destroyed by Growlmon who blasts him into the water causing his own electricity to shock him to death.

Takato and the others end up at a Chuchidarumon village while being attacked by a motorcycle with no rider. During this time, Impmon, now in the digital world as well, meets a Deva who says can help him digivolve. It turns out the motorcycle named Behemoth is possessing a Metalkoromon. Guilmon manages to push it off but in the act gets possessed. In the end Behemoth falls into a pool of lava but emerges once again with the newly evolved Beelzemon as its rider.

Guilmon vanishes due to an experiment. Worried about their digimon Henry and Rika join Takato in the quest of rescuing Guilmon without the help of Terriermon or Renamon. The three find and rescue Guilmon and the warp he was trapped in is destroyed by Hypnos as they escape.

A Musyamon attacks Henry and Takato jumps to the rescue. But Guilmon isn't able to win this battle alone, so Henry has to fight with his own thoughts on the subject of Terriermon Digivolving since last time he couldn't handle the power of Gargomon. When a little girl gets into trouble, Henry acts and Terriermon digivolves to Gargomon. This time Gargomon can control himself and destroys Musyamon. Henry comes to realize that there's just some fights you can't avoid.

Everyone meets and Ryo is introduced to the other group. Meanwhile Rika, hurt and angry, goes elsewhere with Renamon following along. The group eventually gets an idea of where Calumon might be but runs into Makuramon and the dragon deva, Majiramon. Cyberdramon destroys Majiramon and Ryo then leaves the group.

Takato, Henry, and Terriermon are told the secret of Guilmon's birth.

Henry's younger sister, Suzie Wong, arrives in the Digital World and quickly meets Antylamon, the rabbit deva Digimon. As the two become friends Henry, Takato and Terriermon track her down. Makarumon attacks Suzie, but Antylamon fights him off to protect her new friend as Henry, Takato and Terriermon finally arrive. As a result of their new friendship, Suzie becomes Antylamon's Tamer which shocks the others as Suzie is now the Tamer to a Deva. As punishment for her actions, the Digimon Sovereign de-digivolves her back into Lopmon, her Rookie form.

Calumon is being attacked by a digimon and somehow appears in the real world. Meanwhile, a boy named Takato finds a mysterious blue card. His obsession with the Digimon game leads him to create a digimon, and when he finds a Digivice the Digivice copies his created digimon's data and creates a real digi-egg. He has a strange dream involving a Digimon Tamer (who is Rika), and his digi-egg hatches. He finds his created digimon, Guilmon, and fears getting attacked by him.

Calumon watches kids in Takato’s school play soccer and wishes to be a really good soccer player. He convinces Guilmon to come out of his hiding place and play with him. While they’re in the school, a digital field appears and a Vilemon attacks them. Rika and Renamon save them and Rika still thinks digimon are just data and for fighting.

Takato and Guilmon are about to defeat a digimon when Yamaki comes and captures it. Back at Hypnos, they scan the data of the digimon, destroying it and now knowing what Digimon are made of. Armed with this new knowledge, Yamaki prepares to launch the dangerous Juggernaut program to exterminate all the world's Digimon.

Takato is depressed after Henry and Rika have previous commitments and can't go Digimon patrolling, but he feels better when he goes with Guilmon to play with his school friends. But soon the snake deva Digimon attacks, leaving Rika and Henry to fight it on their own, until Impmon helps out and tells Takato they need him. Guilmon and Takato join the battle and Guilmon digivolves to Growlmon. After a short battle, Growlmon mortally wounds Sandiramon with an extra powerful Pyro Blaster, but Sandiramon warns that there's ten more Devas that will be coming before succumbing to his wounds and dying.

Henry was given a worthless card by Kenta's friend Jeramie, but then the card turns into a Blue card when Henry tries to swipe it. When Henry's dad gets home Henry asks if he could check the blue card. While Henry's dad checked it out he notices his old friend Shibumi's code. After Henry, Takato, and Rika go find Jeramie, he tells them that he found the card after bumping into a mysterious man by an electronics store. When Takato and Henry get ready to find the man who bumped into Jeramie, Henry's dad sees them with Terriermon in the park so the kids run away. While Takato, Henry and Rika wait for the mysterious man, they find an Ox and Sheep Deva, Vajramon and Pajiramon. During the battle between Gargomon, Renamon, and the Deva digimons Gargomon Digivolves into Rapidmon to win the battle. Rapidmon destroys Pajiramon the Sheep Deva, but Vajramon, the Ox Deva, secretly reforms himself later and has Renamon come with him to meet with his boss. At the end, Henry's father finds out about Terriermon.

Jeri and her friends go to find Takato, as they hide and discuss how they would be great tamers Jeri drops an impressive collection of digimon cards on the ground. Jeri meets up with Calumon decides she really could be a Tamer and Calumon should be her partner. Calumon is obviously surprised by Jeri's daydream and while reacting to it the Rat Deva Kumbhiramon bioemerges from the ground. They are saved from the Deva by Leomon and Jeri falls in love with the lone warrior. Leomon is weirded out by her plea to be partners and runs away and hides. Takato meets up with Leomon and Leomon confesses he knows nothing about Tamers or partners. Jeri returns and Leomon runs away again. As Jeri is chasing him Takato calls Henry and Rika who come to the park. Kumbhiramon shows up again and Leomon and Gargomon fight him. Jeri tries to use Digimon Cards on him through Takato's Digivice but fails and becomes depressed. Leomon is angered by this and after Gargomon weakens the Deva, he destroys him. Leomon leaves before his sympathy for Jeri can make him stay.

Once the gang enters the digital world Rika spots "satellite" hoping Calamon would be there so they walk along trying to find Calumon but it turns out that the satellite Rika saw were Rock. Just then Meramon attacks and the gang gets separated into two groups: Takato, Guilmon, Henry, Terriermon, Jeri and Leomon in one group and Rika, Renamon, Kazu and Kenta in the other. Meanwhile, Calumon and Makuramon also get separated.

The group returns to the desert to try to find Rika. Rika nearly drowns but is unexpectedly saved by Calumon. A flood pushes them and Renamon to the desert and Calumon digivolves Renamon to Kyubimon to save them. They reunite with the others, but before they can return home, they get confronted by Beelzemon who Kyuubimon realizes is the Digivolved Impmon. Kyubimon digivolves to Taomon to face him, but unfortunately the Dog Deva, Chatsuramon, shows up and recaptures Calumon. Unfortunately, while Yamaki is on leave, the government starts up the Juggernaut, causing sudden night and storms in the Digital World. Thanks to Chatsuramon's attack, Henry, Takato and Terriermon get sucked into a data stream while the others are protected by a shield from Taomon and Beelzemon runs off. At Hypnos as the Juggernaut gets out of control, one of the agents calls Yamaki and Riley and they manage to shut it down.

Calumon helps every digimon in the digital world to Digivolve to Mega so that they could fight their real enemy the D-Reaper. Meanwhile, Kenta meets a MarineAngemon who grows attached to him, but he sends to battle. Azulongmon sends the Tamers to the desert world to return home and while Zhuqiamon is still disgusted by the Tamers Digimons choice, he decides to respect that and allow them to go with the Tamers.

The Tamers returned to the real world. Takato finds out that Jeri’s parents are not coming to get her. He takes the responsibility to return her to her home. On the way to her home, Jeri keeps on acting weird. Takato tries to admit his real feelings for her, but she doesn't even respond to that. Takato left Jeri to her parents and Calumon went with her. Jeri’s father was very angry with her. On the way back Takato heard the news about the D-Reaper which was sighted in the real world. Takato, Henry and Rika decide to return to stop it and sneak off to do so, meeting up in a tunnel that leads to Shinjuku Park.

A mysterious girl arrives with a Digimon Dobermon. They were sent by Azulongmon to make the Tamers able to Biomerge to Mega level. They came to know that Dobermon is a gift and he sacrifices him to make them Biomerge digivolve. They were told that the major part of D-Reaper is in the real world and it's up to them to stop this.