In order to learn Spencer's true intentions, Marcus and ShineGreymon head once again to the Digital World. However, Thomas and the others stay in the human world to fend off the Royal Knights' ongoing attack with Crusadermon this time directing the assault. In the battle, Thomas once again comes across his father, Franz, and Relena....
Craniummon is briefed by Yggdrasil about all the events that occurred up to now while Marcus and the others protect the citzens from the onslaught of lightning from the Digital World. In addition, BanchoLeomon makes the ultimate sacrifice...
In an attempt to defeat Belphemon, Keenan's DNA Charge allows Falcomon to digivolve into Ravemon. Unfortunately, it isn't enough to stop the rampaging Demon Lord. Will Agumon hatch from his digi-egg in time to assist the others and defeat Belphemon once and for all?
Nanami accomplished to drain all the water in the lake, where ElDoradimon rests, drained thus preventing any means of mobility to the Holy Capital. With the fortress's defenses down, Ivan directs a frontal assault but is soon detained by Yoshi and Rosemon. However, the two of them are in for a surprise when they witness that Ivan has gained a power boost.
Both the DATS and the inhabitants of the Holy Capital are preparing for the impending battle. When news arrive that Kurata's camp has been discovered, Marcus takes the initiative to strike a head on assault, but Thomas disagrees since it may be a trap. However, Thomas feels underappreciated witnessing how all the Digimon support Marcus. The forces split with Marcus and Keenan going to engage Kurata while Yoshi and Thomas stay to protect the city. Nanami makes her presence known to Thomas, seducing him in order to make him go astray from his mission.
After their Digivice iC broke, Marcus, Thomas, and Yoshi stumble onto a gym where BanchoLeomon trains them. Can they master their ultimate DNA Charge when Kouki, Nanami, and Ivan attack?
With DATS HQ destroyed and Kurata on his way to the Digital World, the DATS seek out Dr. Crier to ask him to reactivate his digital gate. When they go through, they end up running into Kurata's henchmen: Kouki, Nanami, and Ivan. When their Bio Digimon forms prove too powerful for the DATS to handle, Sampson and Kudamon appear to help out.
The Digimon invasion was temporarily halted due to the efforts of a single man, Kurata, who Sampson knows and who gained the approval of Chief Hashiba. Understanding that Keenan has no place to go, Marcus invites him and Falcomon to stay at his home. Meanwhile, SaberLeomon himself realises in the human world and rampages at an oil refinery as a challenge to the DATS.
To stop Merukimon's further assaults on the human world, DATS authorizes Yoshi, Thomas, and Marcus to be dispatched into the Digital World. Unfortunately, their presence does not go unnoticed by Merukimon and a mysterious shadow, who quickly ambushes the DATS after their arrival. The attacker turns out to be a ten-year-old boy named Keenan, who harbors an intense hatred for humans.
Kristy's made a new friend, a Digimon called Biyomon. Although Marcus feels optimistic for his sister and consents to let Biyomon stay, he's later told that people can't keep a Digimon they've made a relationship with if they aren't DATS members!
Thomas invites Kristy, Marcus, and Agumon to his mansion for lunch. Marcus becomes the unfortunate victim of strange unexplained accidents. Agumon sees the culprit is a Soulmon, who is invisible to everybody else except for him. Marcus and the others do not pay attention to Agumon's warnings, and the pranks become more frequent and more dangerous.
A famous boxer has a fantastic comeback after being absent for some years because of an injury. Thomas is a great fan of his, and when rumors of him using a Digimon to help him in his fights start to spread, he investigates, determined to prove his innocence.
Yoshi is dating a famous musician, Neon Hanamura, who is also her childhood friend. The real reason for her to approach him is because he is suspected of hiding a Keramon (who later digivolves into Kurisarimon), using him to bolster his career.
It's Kristy's birthday and Marcus must attend supplementary exams to save his grades. Unable to be by his sister's side on this day, he asks Thomas to take his place. A Citramon, however, threatens to ruin everything.
Marcus and Thomas, together with their Digimon partners, enter the Digital World to capture Drimogemon. They fall into a large underground labyrinth, Drimogemon's home, and escape seems impossible. Thanks to Marcus' unconventional methods, they manage to leave the labyrinth on Drimogemon's back, but then, the wild Digimon evolves to Digmon.
Marcus and Thomas are ordered to work together, but they aren't able to do so, which becomes clear during the pursuit of a group of Numemon. Suddenly a Drimogemon appears and helps two burglars steal money. Marcus and Thomas try to capture him, but because of their quarreling, he escapes to the Digital World. To capture him, Thomas decides to follow him, even against the orders of Commander Sampson.
Masaru, is a second year Junior High student, and is undefeated in battle, He meets the Digital Monster Agumon, who has escaped from DATS, a secret government organization. Despite terrible first impressions, the two become best friends by talking with their "fists". With others, Masaru and Agumon work to investigate various incidents involving the Digital World and Digital Monsters, to try and get to the bottom of things.