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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 and they think it is hopeless. Takuya's spirit goes into the dumps and he gets very angry. 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. Then Patamon, Salamon, and Lopmon go into a trance and the Three Guardian Angels appear in spirit form above them. They speak to the kids about how they are the last chance the Digital World has and that the future now lies in their hands again. The five kids use their Digivices and activate the Ancient Spirit Evolution. All five kids join together in Susanomon, the Warrior of Peace. They fly up and drag Lucemon away from the Human World just as he pierces the surface. Lucemon begins to breathe fire everywhere and the kids remember Cherubimon told them that Lucemon can't think coherently. Takuya thinks that it has something to do with the black orb so they fly towards it and see the Lucemon Larva.

Koji is clutching his stomach from the new spirits and Takuya is raging after Lucemon. The two are enveloped in a fiery cocoon where they merge together with all twenty spirits. Susanomon emerges and the final battle between good and evil soon begins. Lucemon launches at the new Digimon but is ineffective. He then uses his powers of Light and Dark to envelop Susanomon. Koji and Takuya fight the effects and De-Digivolve to break free.

The gang turned into their human-fusion spirits to go after Lucemon but he defeats them all, thus returning the friends into their human form again. 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 it was all over, Koichi gave his human and beast spirit to Koji and afterwards, Koji and Takuya transformed as one into the ancient Digimon, Susanomon.

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. Meanwhile, Crusadermon asks Lucemon if the Royal Knights still had an agreement to take them to the Human World but Lucemon sends them on their way. Later that night, the search continues and Takuya accidentally makes some books fall during the search and then he falls asleep. The group reunites but no one had located the key. The next morning, the Royal Knights appear and start to attack.

With only two sections of the Digital World remaining, the Royal Knights are on the hunt for the next fractal code. Since no one knows where the fractal code in Ophanimon's castle is, the Digidestined have set up a post at the Autumn Leaf Fair. JP is operating a large machine to rearrange the order of the town, therefore breaking up the fractal code to make it harder for the Royal Knights to locate. The Royal Knights delete the Digimon, so Takuya and Koji unified-spirit-evolve to KaiserGreymon and MagnaGarurumon to face them together. Dynasmon pounds the ground and is furious to only find one piece of the fractal code and starts to hunt for more. KaiserGreymon goes in to attack Dynasmon while MagnaGarurumon continues his assault on Crusadermon.

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. However, the Palmon doesn't know and all four are destroyed. 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. Takuya and the gang arrive at Flame Terminal where a group of Poyomon, Pagumon, Biyomon, and Elecmon are starting to worry and a Pagumon starts losing faith on the Legendary Warriors.

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 so the gang helps Swanmon feed the babies. When the group gets back they find that the Royal Knights are at the village. Takuya and Koji Unify Spirit evolve to hold them back while the rest of gang try to save the digieggs and Zoe tries to get the Trailmon to help out. This time they agree and the babies are loaded on. Takuya and Koji get badly beaten and end up reverting to their human forms but the babies protect them by using bubble blow.

The Royal Knights arrive at Beanstalk Village where the captured children encountered an unconscious Mamemon. Dynasmon locks Tommy and the children in a cell until they reveal where the "key" is. Meanwhile, Takuya and the gang make a ramp to cross the gap. Worm the Trailmon reveals that the route to Beanstalk Village is a very tough trek. And back at Mamemon Village, 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.

After being blasted away by Dynasmon's attack, the kids awake to find themselves on the blue moon, one of the three moons above the Digital World. They hitch a ride with a Starmon to a space station where SuperStarmon leads the Starmon in a large operation. After KendoGarurumon tries and can't escape, they learn there is a force field surrounding the moon preventing their exit. The kids, along with the help of SuperStarmon, the Hamburgermon, and the Meteormon, construct a rocket that worthy of flight. As they launch, they can't quite make it so Takuya evolves to BurningGreymon and gives them the extra boost needed. As they arrive back on the Digital World, they prepare to face the Royal Knights once more.

Now that Cherubimon has absorbed all the information of the Digital World, he transforms into a very strong and hard to defeat opponent but EmperorGreymon and MagnaGarurumon try their best to stop him. Although, they are no match for him since he has all of the data. Takuya fires his attack at Cherubimon making the whole bottom half of Cherubimon disappear but it regenerates. Koji then realizes that to kill Cherubimon they must strike the head where the data is kept. Takuya, as EmperorGreymon, manages to reach Cherubimon and stabs the head, releasing the data and mortally wounding him. It's then revealed that the true enemy is Lucemon and he releases his Royal Knights to finish the job that Cherubimon failed.

The Digidestined meet up with Ophanimon, who is currently trapped in a cage of light and facing off against Cherubimon. After Agunimon, Lobomon, Kumamon, Kazemon, Beetlemon, and Loweemon try their attacks in vein, they soon learn that their powers are weakened. Agunimon and Lobomon go back to Takuya and Koji, then fusion-evolve, grabbing Cherubimon and carrying him outside where they can have a final confrontation. Meanwhile, the other four legendary warriors set to work on freeing Ophanimon and decide to break the mirrors that are refracting the light from his cage. However, Aldamon and BeoWolfmon are no match for Cherubimon as he absorbs their D-tectors. As Takuya and Koji are barely hanging on, Cherubimon bursts back into the castle and attacks the warriors.

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 who means them no harm. 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. However, Cherubimon felt outnumbered because he was the only beast type Digimon while Seraphimon and Ophanimon were human types. Cherubimon believed that Seraphimon and Ophanimon plotted against him and so he led the beast type Digimon into a war against the humans. When Seraphimon was injured, Ophanimon used her power to heal him and after much destruction the three angel guardians were sealed away. Cherubimon, though, had five spirits under his control and used them to create the evil legendary warriors.

Duskmon finally realized that he had a human brother, Koji, and didn't want to fight him. So Cherubimon corrupted him with more dark memories of his past to turn him against Koji. Meanwhile, Zoe, Tommy and J.P. tried to contact the others about the Rose Morning Star, where Ophanimon was being held captive. Bokomon and Neemon went and found Patamon but they also found Takuya as well. Unfortunately, Velgemon showed up and revealed to Koji his secrets and made him afraid of attacking his brother which gave Velgemon the upper hand. Luckily, Takuya rescued Koji just in time and convinced Koji that the only way to save Koichi was to defeat his Spirit of Darkness. Both Takuya and Koji Fusion Evolved to Aldamon and Beowolfmon and knocked the Legendery Warrior of Darkness out. Unfortunately, Velgemon showed up, and revealed to Koji of his secrets, and made him afraid of attacking his brother, which gave Velgemon a temporary upper hand. Luckily, Takuya rescued Koji just in time, and convinced Koji that the only way to save Koichi was to defeat his Spirit of Darkness out of him! Both Takuya and Koji Fusion Evolved to Aldamon and Beowolfmon, and knocked the Legendery Warrior of Darkness out of his misery! Man, weren't they good or what?!

After the gang finally got back together again, Koji decides to run off after Velgemon to find out their connection and Takuya chases after him. 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. He finally spills the beans and tells them that Ophanimon is being held in a castle.

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. When Duskmon's Beast Spirit Evolved to Velgemon, he forgot what little he still knew and tried to destroy Koji. Thank goodness Ophanimon intervened in time to stop him and now Koichi remembers that Koji is his brother.

When we last left Koji, he had Fusion Evolved into Beowolfmon and was trying to catch up with Duskmon. He wanted some answers but the baddie gave him the slip. 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. It looked bad for our heroes until Aldamon figured out that by combining their attacks they might get the upper hand. Mixing up their powers confused Sephirothmon and brought on his defeat.

It's bad enough when Mercurymon corners you in a world of mirrors and beats you up 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. Takuya returned to the others and the Digi-Egg finally hatched but inside was only a Patamon. And what good is that little guy gonna be against all the forces of darkness?

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. Duskmon was about to destroy Koji, when Bokomon's "baby" unleashed a new power source. Lobomon & KendoGarurumon Fusion Evolved into BeoWolfmon. Meanwhile, Takuya battled and beat IceLeomon but couldn't get to Koji in time to help.

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. When she breaks the spell, she and Ranamon wind up digivolving into their Beast forms. Zoe destroys Ranamon and collects both her spirits before she is freed. Meanwhile, Takuya wanders into the Thunder Sphere, where he encounters Parrotmon, and J.P. gets lost in the Wood Sphere, where he finds Cherrymon but both the boys manage to defeat their opponents with ease.

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 Asuramon was more than willing to help. Meanwhile, Koji was plagued by his deepest fears about friendship. Karatenmon thought he got the best of him but he didn't count on KendoGarurumon. As it turns out, Asuramon was just pretending to be Tommy's friend so he could steal his Spirit but Tommy Spirit Evolved to Korikakumon and digitized that three-faced freak!

Having survived his weird 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 isn't a game, it's serious. As was the trouble that J.P., Zoe and Tommy were in, they were being tickle-tortured by Mercurymon & Ranamon. Then, out of nowhere, Lobomon appeared to try and save them but he was still too weak from the battle with Duskmon. When it seemed like it was all over, a new and more powerful Agunimon arrived with the power of nature as his ally. He saved his friends and sent the bad guys packing.

Feeling guilty about what happened to his friends, Takuya took Dark Trailmon back to the real world. However, on the way home he turned into this freaky half-human, half-Digimon. Then, 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 but Duskmon kept getting in the way. Takuya finally realized he couldn't run from his fears, so he decided to go back to the Digital World to face the music.

While on the way to the Rose Morning Star, our heroes got dumped at the Dark Gate, the creepy entrance to the Continent of Darkness. Meanwhile, Cherubimon called a meeting of the Legendary Lunkheads. After a little encouragement, Arbormon decided it was time to get rid of the gang once and for all but the Warrior of Wood was no match for our heroes. They chopped him down and stole his Beast Spirit. Then, out of nowhere, Duskmon showed up and destroyed Arbormon.

The gang headed to Hamburgermon Village, hoping to enjoy some of their famous burgers. However Petaldramon and his cronies had ravaged the hamlet on a quest for the ultimate burger, taking the town's top burgermeister hostage in the process. Our heroes decided to help the missing man's family by creating their own burger masterpieces. Fortunately, Tommy made a burger the beasties liked but in doing so, they took Tommy, Zoe, and JP away too. Eventually the kids saved the day and reunited the Hamburgermon family.

On their way to the Rose Morning Star, the gang made an unscheduled stop at the Great Trailmon Race. Everyone decided to join the festivities and partnered up with a Trailmon. Bokomon was a little too busy playing 'mother hen' to participate. During the wacky ride, ShadowWereGarurumon & Dogmon used all kinds of nasty tricks to take the gang out, one by one. Finally, Takuya Beast Spirit Evolved to BurningGreymon and gave that mean old wolf & his mutt a taste of their own medicine. With the two of them out of the way, Takuya & Worm crossed the finish line first!

After crashing their raft about a million times, 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. When out looking, he found the Toucanmon and saved their lives but those jerks just ran off again. Then a big fight broke out between Datamon & Petaldramon. Datamon gave the guys their D-Tectors back and they sent Petaldramon packing. Now that they have their D-Tectors again, everything seems great but that probably won't last long.

The Digidestined hunted high and low for their D-Tectors but those birdbrained Toucanmon flew off with them. When they tried to swim after the birds, some Gomamon stopped them, which was good because they were about to swim into some nasty whirlpools. So they all set sail on a raft they built and of course, Ranamon attacked. She knocked Kazemon to the ocean floor, but there, Zoe found her Beast Spirit and evolved into Zephyrmon. The whirlpool calmed and the beast Calmaramon was defeated but the guys' D-Tectors were still gone.

After Whamon dropped the gang off, they decided to take a little vacation at Toucanmon Paradise. But the food and free beach gear was part of a plot to separate the boys from their D-Tectors in order to win favor with the evil Warrior of Water. When Ranamon showed up, Zoe was the only one able to Spirit Evolve. Kazemon was holding her own, until Ranamon found her Beast Spirit and Calmaramon overpowered Kazemon.

Finally, the guys made it to Forest Terminal but no one was there. Down the road at a castle they met Socerimon & Seraphimon, who told everyone how the Legendary Warriors came to be. Then Grumblemon and the other goons attacked! Mercurymon beat Seraphimon and all that was left of him was a Digi-Egg. Takuya & the others escaped on a Trailmon but Socerimon stayed behind to fight. Now they are left alone with the Digi-Egg and they don't even know what to do with it until Ophanimon is found.

When Takuya Beast Spirit Evolved to BurningGreymon, he couldn't control himself. So Beetlemon & KendoGarurumon tried to help him but were pretty useless. It finally took a lot of reasoning from little Tommy to get Takuya to tame the Beast within. Then the gang got stuck in the mud and Grumblemon showed up to grab Tommy. So Takuya Beast Spirit Evolved and did some grabbing of his own. He took Gigasmon's Spirit and returned Kumamon's to Tommy. Grumblemon escaped and met up with the Evil Legendary Warriors (Ranamon, Mercurymon, Arbormon, Duskmon).

Bokomon took the gang to get their futures told by Shamanmon, the fortune teller. Just as Shamanmon started the premonition tango, Grumblemon attacked and this time he brought a friend. With the strength of Golemon behind him, Grumblemon stole Tommy's Spirit. BurningGreymon joined in on the fight but he didn't know the difference between good guys and bad. Gogglehead figured out that it was Shamanmon possessed by a Beast Spirit but when he freed Shamanmon, the Beast Spirit possessed him instead! Then when he started attacking his friends, Koji had to Digivolve to KendoGarurumon to stop him.

The gang finally got back together on the edge of the Forest Kingdom. Starving and tired, they decided to make camp and chow down. Then, they discovered the forest was full of these freaky trees that showed them video from the real world! 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. Koji & Takuya finally figured it out, so they Spirit Evolved and ended the digital nightmare! Koji then received a weird e-mail on his D-Tector.

On their way to the Forest Kingdom, J.P., Zoe, Bokomon & Neemon came upon a school for young Digimon. There, they met Tsunomon, a little guy who didn't get along with the other kids. Then storm came through and almost washed away the school. Zoe & J.P. Spirit Evolved just in time but while they were busy, Gabumon got swept away. With a little convincing from the guys, Tsunomon Digivolved to Gabumon and saved his friend! After that, Gabumon was the most popular kid in school.

After losing the fight with Grumblemon, Takuya, Koji & Tommy fell into a world of living toys, where they all fought with each other! Then an overgrown teddy bear (WaruMonzaemon), working for the ShadowToyAgumon, captured Tommy. Takuya & Koji Spirit Evolved and made quick work of the bad toys but when they got to Tommy, he was playing with his captor (Monzaemon). At least they got a free ride to the Forest Kingdom and now all they need to do is find the rest of the gang!

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! Turns out the creep who stole the women is also a Legendary Warrior. Grumblemon has the power to Beast Spirit Evolve to Gigasmon and he defeated our heroes. With the gang split up, it looks like the Forest Terminal will have to wait until they find each other.

On the way to the Forest Terminal the gang winds up at Wind Factory. There, they meet the Kokuwamon, a group of machine Digimon who are being forced into slave labor by the Goblimon. So Takuya comes up with a plan to save the little guys but once the fighting starts, they meet the head honcho, Snimon. When the Spirit of Thunder is uncovered, J.P. jumps at the chance to Spirit Evolve into Beetlemon and then uses his Thunder Fist to squash Snimon.

After the battle, Takuya doesn't remember what happened but he obtained a Digicode that reconnects Digimon city. J.P. and Tommy get separated from the group and they try to return to their world but find themselves in a labyrinth. The two desperately try to Digivolve but are soon captured by Pagumon Digimons. Koji acquires the Digispirit that transforms him into Lobomon and he tries to save J.P. and Tommy from Pagumons and Raremon.

Takuya, Koji, Zoe, Tommy and J.P. are contacted through their cell phones (that later on transform to their Digivices) to go to the Digiworld. They take a train at an underground terminal and 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 who battles Cerberusmon.