Takuya, Koji, Zoe, Tommy and J.P. descend to the Digiworld where they are confronted by Cerberusmon. Takuya's Digivice is activated and the Digispirit of his Digimon is called, transforming him into Agunimon for battle.
After the battle, Takuya doesn't remember what happened but he obtained a Digicode. J.P. and Tommy get separated from the group and are soon captured by Pagumon Digimons. Meanwhile Koji acquires the Digispirit and he tries to save J.P. and Tommy.
Neemon told the gang they could take the train back to reality but they all decided to stick it out in the Digital World. Things were going well until they find the marks of the Ten Legendary Warriors and even worse, they were interrupted by the Candlemon Tribe!
The gang tries to hitch a ride to the Forest Terminal but while deciding which way to go the group splits up. Zoe, J.P., Neemon, and Bokomon end up in Breezy Village. Zoe needs to Spirit Evolve when the Fungus Brothers Digivolve but it doesn't go well.
While trying to find food, the gang met up with the Shellnumemon and they agreed to help rescue the women from the evil Grumblemon. When they told the snails they were Legendary Warriors, they were captured and traded for the women!
After losing the fight with Grumblemon, Takuya, Koji & Tommy fell into a world of living toys, where they all fought with each other! Takuya & Koji Spirit Evolved and made quick work of the bad toys but when they found the previously abducted Tommy, he was playing with his captor (Monzaemon).
On their way to the Forest Kingdom, J.P., Zoe, Bokomon & Neemon came upon a school for young Digimon. A big storm came through and almost washed away the school but Zoe & J.P. Spirit Evolved just in time.
Starving and tired, the gang decided to make camp but soon discovered the forest was full of these freaky trees. While sleeping, Tapirmon came under the influence of Kepyrmon, who planted bad dreams into a sleeping Tommy. Convinced everyone was against him, he Spirit Evolved to Kumamon and took on his friends.
After getting this weird e-mail, Koji broke away from the group with Neemon & Bokomon tagging along. The 3 of them ran into Gotsumon, a rock Digimon, who was looking to awaken the Spirit. Then, their old pal Grumblemon came back for some more fun. When Takuya and the rest of the gang arrived, Gigasmon defeated them and ended up taking Zoe's Spirit!
Bokomon took the gang to get their futures told by Shamanmon, the fortune teller and just as Shamanmon started, Grumblemon attacked. With the strength of Golemon behind him, Grumblemon stole Tommy's Spirit. Gogglehead figured out that it was Shamanmon possessed by a Beast Spirit but when he freed Shamanmon, the Beast Spirit possessed him instead!
When Takuya Beast Spirit Evolved to BurningGreymon, he couldn't control himself. It finally took a lot of reasoning from little Tommy to get Takuya to tame the Beast within. Grumblemon showed up and grabbed Tommy but he eventually escaped and met up with the Evil Legendary Warriors.
The guys made it to Forest Terminal but no one was there. Down the road at a castle they met Socerimon & Seraphimon just as Grumblemon and the other goons attack! Mercurymon beat Seraphimon and all that was left was a Digi-Egg. Takuya & the others escaped but now they are left alone without anything but the Digi-Egg.
After the wild ride on a Trailmon, our heroes find themselves trapped in an underground cavern. Unfortunately, Arbormon & Grumblemon figured out where they were and attacked. Grumblemon unleashed an angry horde of Golemon and it looked like the Digidestined were doomed.
The gang decided to take a little vacation only to find out that the food and free beach gear was part of a plot to separate them from their D-Tectors. Then when Ranamon shows up, Zoe was the only one able to Spirit Evolve.
The Digidestined hunted for their D-Tectors but those Toucanmon flew off with them. So they all set sail on a raft they built but of course, Ranamon attacked. She knocked Kazemon to the ocean floor, but there, Zoe found her Beast Spirit and evolved into Zephyrmon.
The gang finally made it to the Autumn Leaf Fair but they still couldn't find the Toucanmon. Tommy found out that Datamon had the D-Tectors and needed something to trade for them. Then a big fight broke out between Datamon & Petaldramon. Datamon gave the guys their D-Tectors back and they sent Petaldramon packing.
On their way to the Rose Morning Star, the gang made a stop at the Great Trailmon Race. Everyone decided to join the festivities and partnered up with a Trailmon. During the wacky ride, ShadowWereGarurumon & Dogmon used all kinds of nasty tricks to take the gang out, one by one.
The gang headed to Hamburgermon Village but Petaldramon and his cronies had ravaged the hamlet, taking the town's top burgermeister hostage in the process. Our heroes decided to help the missing man's family but in doing so, they took Tommy, Zoe, and JP away too.
While on the way to the Rose Morning Star, our heroes got dumped at the Dark Gate. Cherubimon called a meeting of the Legendary Lunkheads and Arbormon decided it was time to get rid of the gang once and for all.
Not only did Duskmon throw BurningGreymon around, he took the Digidestined to task without even flinching. Later, Takuya came up with a plan to defeat him but that just started an argument with Koji. Things started getting even weirder, it was like Duskmon was in pain and then darkness covered everyone.
Takuya took Dark Trailmon back to the real world. However, on the way home he turned into this freaky half-human, half-Digimon. To make matters worse, Takuya returned to the same day he left for the Digital World. Thinking everything would go back to normal if he never left, Takuya tried to stop himself from getting on the train.
Having survived his trip to the Real World, Takuya returned to the Digital World on a mission. He realized that being a Digimon may be fun but it's also serious. As was the trouble that J.P., Zoe and Tommy were in. Then, Lobomon appeared to try and save them but he was still too weak from the battle with Duskmon.
The gang headed off to the Rose Morning Star but the trip was cut short because the kids were sucked into Sephirothmon. While trying to find an exit, J.P. was pushed into another dimension. Then his own shadow appeared with thousands of evil clones of his friends, telling him they never really liked him in the first place. J.P.
Sephirothmon decided the guys needed a little one-on-one attention, so he split them up to face their personal demons. Tommy had some unresolved stuff with his brother to work out and Koji was plagued by his deepest fears about friendship.
Zoe is stuck in the Water Sphere, where she has a flashback about being teased. She soon finds a group of Honeybeemon who are attempting to capture her for Ranamon. Ranamon later forces them to feed Zoe an apple that causes nightmare visions. Meanwhile, Takuya wanders into the Thunder Sphere, where he encounters Parrotmon, and J.P. gets lost in the Wood Sphere, where he finds Cherrymon.
Koji & Takuya are still stuck inside the Sephirothmon. Zoe, J.P. and Tommy Spirit Evolved to help them but they couldn't get back inside. Unfortunately, Duskmon is desperate to determine his connection to Koji and he squeezes Koji's memories about his dad & step-mom out of him. Meanwhile, Takuya battled and beat IceLeomon but can't get to Koji in time to help.
It's bad enough when Mercurymon corners you in a world of mirrors but then he uses Seraphimon's data to turn into ShadowSeraphimon. It looked really bad for Takuya but energy from Seraphimon's Digi-Egg let Takuya Fusion Evolve to Aldamon, who kicked the fractal code out of ShadowSeraphimon and Mercurymon.
When we last left Koji, he had Fusion Evolved into Beowolfmon and was trying to catch up with Duskmon. Meanwhile, as everyone was celebrating the birth of Patamon, Sephirothmon decided to crash the party. He used the gang's own attacks against them so he could take away their spirits.
As the battle between Duskmon & Beowolfmon raged on, Patamon was doing his best to lead the gang to Koji but Cherubimon had them trapped. Then Cherubimon took advantage of Koichi's amnesia and gave Duskmon his Beast Spirit.
After the gang finally got back together, Koji runs off after Velgemon to find out their connection. Meanwhile, Zoe, J.P., and Tommy decide to find some information about the Rose Morning Star and they find a Trailmon that has some information but he wants a few favors first.
Duskmon finally realized that he had a human brother, Koji, so Cherubimon corrupted him with more dark memories of his past. Zoe, Tommy and J.P. tried to contact the others about the Rose Morning Star and Bokomon and Neemon went to find Patamon.
Waking up from a dreadful nightmare was terrible for Koji and Koichi but more than that, Koichi realized that Cherubimon used him for his own purposes. He felt guilty for hurting his brother and friends. En route to the Rose Morning Star, Patamon told Koichi that Light and Darkness are brothers and exists for each other.
With a new goal in mind, the Digidestined kids arrive at the Rose Morning Star. After defeating two Phantomons to gain entry, they are greeted by Goatmon, a wise Digimon. He tells them of the ancient times and why Cherubimon was tainted. It turns out after Lucemon's defeat, the three angel guardians lived in peace.
The Digidestined meet up with Ophanimon, who is currently facing off against Cherubimon. After trying their attacks in vein, they soon learn that their powers are weakened. Agunimon and Lobomon go back to Takuya and Koji, then fusion-evolve for a final confrontation with Cherubimon. Meanwhile, the other four legendary warriors set to work on freeing Ophanimon.
Takuya and Koji spirit evolved together and fly the others to safety. The two are powerful and actually winning the battle against Cherubimon. On the sidelines the others are cheering them on, except Koichi. He's feeling guilty that he can't help his brother. Cherubimon is fading and after one final blow, he's down but then the castle starts to crumble.
Now that Cherubimon has absorbed all the information of the Digital World, he transforms into a very tough opponent but EmperorGreymon and MagnaGarurumon try their best. Takuya fires his attack at Cherubimon making the bottom half of Cherubimon disappear but it regenerates.
With Cherubimon defeated, the Digidestined are happier than ever. As they try to sort things out, they arrive at a large tunnel entrance where they meet a helpful Baromon. Baromon leads everyone into the Tunnel of Time, where the Digital World's history is kept and tells them of Lucemon's treachery.
After being blasted away by Dynasmon's attack, the kids awake to find themselves on the blue moon. They hitch a ride with a Starmon to a space station. After KendoGarurumon tries and can't escape, they learn there is a force field surrounding the moon preventing their exit. The kids, with the help of friends, construct a rocket that worthy of flight.
Dynasmon locks Tommy and the children in a cell until they reveal where the 'key' is. As the kids try and escape by throwing a bomb at the cell bars, Dynasmon grabs the Elder and forces them to tell the Royal Knights where the "key" is.
The gang ends up at the Village of Beginnings where Digimon are born. They are introduced to Swanmon who takes care of all the babies. There are lots of them because the Trailmon are too scared to take them to their families. When the group gets back they find that the Royal Knights are at the village.
After the Village of Beginnings is destroyed, a group of Poyomon warns Takuya that the Flame Town Terminal is going to be attacked. A SkullSatamon grabs a Palmon, questioning where the Digi-Code near Flame Terminal is. Then he questions a Gazimon hiding in a bush and he says it's in the temple. SkullSatamon sends an attack into the temple and absorbs the Digi-Code.
The Royal Knights destroy another area and send the Digi-Code to Lucemon. Gotsumon defends the sacred jewels at the Gotsumon Village. Koji decides that Gotsumon should come with them since he wants to help fight the Royal Knights. The Royal Knights arrive at the Forest Area where Seraphimon's Castle is but a barrier protects it.
KaiserGreymon and MagnaGarurumon, along with the rest, arrive at Ophanimon's Castle. When they enter the Castle, they encounter the Castle librarian and caretaker Nefertimon on the balcony. She has no clue on where the Digi-Code key is so the gang splits up.
The kids are on one of the 3 Digital Moons and Koichi is still shocked about what Crusadermon said to him. The Royal Knights still question Lucemon if they still had an agreement to take them to earth. And before the Royal Knights arrive, Takuya remembers the challenges he and the rest had in their adventures.
With Lucemon about to destroy Takuya, Zoe, J.P. Tommy and Koji once and for all, Lowemon steps in to stop the attack. Lowemon let the darkness and the light flow into one and surround him. When the battle was over, Koji and Takuya transformed as one into the ancient Digimon, Susanomon.
Koji is clutching his stomach from the new spirits and Takuya is raging after Lucemon. Susanomon emerges and the final battle between good and evil soon begins. Lucemon uses his powers of Light and Dark to envelop Susanomon. Koji and Takuya fight the effects and De-Digivolve to break free.
All the kids are down in the train station after getting pummeled by Lucemon. Takuya gets ready to fight again, however, the others stop him because Lucemon was able to regenerate. Then, Agunimon appears out of the Digivice and helps Takuya gain the strength needed to accomplish his task. The other Legendary Spirits all fly out of the Digivices and help their respective Digidestined.