Ken, angry at his inability to control SkullGreymon, works on his Dark Ring. Wormmon, in the hope that Ken might use him in his experiments, frees Agumon. However, as he reunites with Tai, Ken captures him with his new Dark Spiral, and makes him dark digivolve into MetalGreymon and attack the DigiDestined.

The digital adventure continues as three new DigiDestined (Davis, Yolei, and Cody), receive their digivices and Davis meets Veemon, his partner. Veemon armor digivolves into Flamedramon to fight off a Monochromon being controlled by the evil Digimon Emperor.

Tai and Agumon land on a snow-covered island and are forced to defeat a Frigimon. After destroying the Black Gear that was controlling him, they cross over to the island where Matt and Gabumon landed. Meanwhile, Matt goes out to search for his brother against Gabumon's advice and gets hypothermia. Once the two boys meet up, they end up fighting each other until a Mojyamon attacks them. They defeat the Mojyamon and expel the Black Gear that was controlling him.

The kids meet the ruler of File Island, Devimon, the controller of the Black Gears. He, along with Ogremon and a possessed Leomon, attack the kids who manage to escape. They end up in a mysterious mansion, which proves to be a hallucination created by Devimon. Devimon breaks File Island into multiple, smaller islands and separates the kids onto the different islands.

Apocalymon launches the "Total Annihilation" attack, the power within the kids causes their digivices to contain the blast and return it back at full force onto Apocalymon and with that the final battle is over. Gennai shows up and tells the kids that the DigiWorld will now start over, starting with File Island. The DigiWorld begins to return to normal and the kids go back to File Island. They decide they will stay in the DigiWorld the rest of the summer since time on Earth is so much slower than the DigiWorld. However, Gennai explains that after Apocalymon was destroyed time in the real world and the DigiWorld became equal, so now time travels at the same rate in both worlds. The only way for the kids to get home is through a portal that will close in two hours. Each of the kids must say goodbye to their Digimon partners. However, as they are leaving, T.K. and Kari somehow seem to know that they will see each other again someday. Tai says that he will never forget the digimon and wonders if they will remember him when or if they meet again!!!

What is left of Spiral Mountain begains to fall apart and the kids soon find themselves floating in darkness. Gennai tells the kids that the evil force that made the DarkMasters came from the fire wall. This evil force walked across the fire wall and threatened the end of the Digital World. There were other DigiDestined children who had defeated this evil before. Tai and the others where choosen because a new evil had come to the DigiWorld from behind the firewall. It was said that the DigiWorld would be put into darkness, this is where the kids are floating right now. Gennai gets cut off before he has a chance to tell the kids the name of the evil force. Soon the new evil appears, Apocalymon, who has all of the attacks of the DarkMasters combined. Aploycomon destroys all of the kids crests to stop the Digimon from digivolving. The kids are then sent to the "Data World" where all computer information comes from. The kids finally realize just how inprotant each of them really are to the DigiWorld, this then restores the power of their crests and they return to the "Non-Data World". This is it, now only the finally battle remains...Stay Tuned for next time…

Piedmon starts to get very upset when the Digimon try to fight him and actually starts turning the kids and Digimon into keychains. Everyone is captured except for Kari and T.K. T.K. calls for Angemon and Angemon digivolves into MagnaAngemon and saves the two kids. MangaAngemon gets back all the keycains and returns everyone to normal. Piedmon attacks with an army of Vilemon and at the save time, Mimi arrives with an army of Digimon. Soon the evil forces and Piedmon are defeated. They kids think they have won, but Gennai sends them an email that tells them that the DarkMasters were not the real evil force in the DigiWorld. There is an other evil force that created the DarkMasters. The kids will still have to face this TRUE evil force latter on.

Joe and Gomamon are on a beach away from everything and everyone else, they start looking for Matt and after a while they do find his boat. Matt is now where around. Meanwhile, WarGreymon fights Piedmon but he needs the help of the other Digimon and fast. Matt thinks that he is not needed anymore and his fear creates a cave that he is soon lost in. Gabumon finally gets Matt to realize that he really is needed by the others and the cave soon disappears. Sora ends up in the same type of cave after finding Matt's boat but not him..she becomes very depressed. The others find her and climb down in to save her. They help her to understand what she must do to make this cave disappear and soon she is free. Everyone then goes to help Tai in the battle against Piedmon. Gabumon gains more power after Matt realizes that he and Tai are better friends now than ever before.

The kids again split into two groups to prepare for battle with the final Dark Master. Tai and his group are attacked by LadyDevimon. Tai tells Sora and T.K. to find the others (Joe and Mimi). Joe and Mini find Elecmon in the now destroyed Primery Village and joins them on the quest for the final battle. Joe and Gomamon decide to go off by themselves for a while to see if they can find their own place in the world. With the help of WarGreymon, Tai and the rest of his group defeat LadyDevimon. Shortly after they defeated LadyDevimon, the last DarkMaster, Piedmon appears.

As the building caves in on them, the kids fall into the sewers under the city. Tai and Izzy have the medicine for Kari and are searching for them. Sora, Biyomon, and Patamon find Kari, T.K. and Gatomon. Kari's fever finally breaks and she wakes up, feeling a little better than before. The group continue to search for Tai and Izzy but run into a group of WaruMonzaemon. The stange light that took over Kari before returns and helps make the Digimon stronger than ever before. The group defeats the evil Digimon and free some enslaved Numomon. While the kids follow that light, Machinedramon arrives and battles the WarMonzaemon. Still looking for Kari and the others, Tai and Izzy run into Andromon and are attacked by Machinedramon, after all of this, the two groups of kids finally meet up. Kari's "light" gives WarGreymon all the power he needs to finally defeat Machinedramon.

The kids are crossing yet another desert, but Kari gets sick and passes out. Tai gets really upset and soon Tai tells the others that Kari almost died once. When Tai and Kari were younger, Kari was sick at home and Tai was to be keeping an eye on her. Thinking of only himself, he took her outside just so he could play with his friends. Kari ended up in the hospital for a while as a result of not being kept indoors. After knowing this, the kids look for a hospital in the Digital World to take Kari or a place that has medicine to help her. Kabuterimon takes them to a deserted city where Kari can rest, but they still need to find medicine for her. Using the internet, Izzy locates a place where they can get the medicine. He soon realizes that the evil Digimon are able to find them whenever he uses his computer on a network. Soon, the bad guys are all over and Izzy tries to throw them off by using the computer again. The grab the medicine and return to where Kari and the others were...but they arrive just in time to see the building be destroyed by a missile. It turns out that the other kids got out just before the missile arrived. The others are chased into another building which crumbles in on top of them.

Mimi and Joe find SaberLeomon, the Digivolved form of Leomon. SaberLeomon takes Joe and Mimi to a safe place where they meet with Otamamon and Gekomon. Puppetmon tells the other kids to follow him is they want to defeat him. They follow him, but he leads them to a group of Red Vegiemon, but they are no match for the kids and digimon. An angered Puppetmon makes his house come to life in an attempt to crush the kids. Leomon digivolves back into SaberLeomon and fights MetalEtemon. Ikkakumon digivolves into Zudomon to help in the battle. Puppetmon tries to get MetalGarurumon to attack the kids like before, but instead, he destroys Puppetmon. Just before Puppetmon disappears for good, he is told that the kids have friends and he doesn't, so he could have never won the battle. Leomon is defeated and is gone. Joe, Mimi, and Ogremon say that they WILL defeat the Dark Masters…or what's left of them anyway.

The Woodmon are chasing Ogremon trying to catch him so they can take his digital data. Ogremon is then traped under a tree when a giant meteor slams into the ground. The Woodmon all run away and Joe and Mimi show up and help Ogremon. At first, Ogremon didn't want their help, but over time he becomes their friend. The other kids find their way into Puppetmon's house and begin to look around. However, outside the house Puppetmon finds Joe and Mimi, unlikely as it is, MetalEtemon shows up and saves them. Back inside the house, Tai and the other kids find two of Puppetmon's guards. One of the guards leads them to a cannon that can be used against Puppetmon. Finally, as exspected, MetalEtomon turns on Joe and Mimi and chases them through the Jungle, but during the case something that looks like Leomon appears.

Matt doesn't understand why they have to be in the DigitalWorld and we wants to leave RIGHT NOW! (Yes, he has BIG issues right now) MetalGarurumon and WarGreymon battle while Matt and Tai have a fist fight. This was Puppertmon's plan all along, to get all the DigiDestined to destroy each other. A strange light suddenly appears and takes over Kari's body. The kids find themselves flying through the air and are surrounded by computer images from the past. They learn that the crests represent the best quality each of them had four years ago. Finally, they are told how and why each of them where chosen to be a DigiDestined. If any of the kid's special quality is ever lost, that child's Digimon can no longer Digivolve. After that was all over, Kari returned to normal, but was very weak and tired. Matt still wants to be alone and leaves again. Mimi doesn't want to go on with the goup either and stays behind too. Joe doesn't think that Mimi will be safe by herself and stays with her. They rest of the group go on their way...once again leaving the group split up again.

Tai and everyone else gose off to look for Matt. Matt is not really sure why he is a DigiDestined and gets upset that the others are getting stronger and better then he is (or so he thinks..he's sort of loosing is mind at this point..oh, sorry). Anyway, a tree-like Digimon called Cherrymon, tells him that he must be the leader and in order to be the leader, he must destroy Tai. Puppetmon and Garbagemon attack the others. The kids are having problems with the battle, until Matt shows up with MetalGarurumon and blast away the Garbagemon. Then, as if things weren't bad enough, MetalGarurumon turns on Agumon (at Matt's decision) and challenges him to a fight.

WarGreymon isn't doing so well and is about to be destroyed. Just in time, Whamon jumps out of the water and takes the blast ment for WarGreymon. Whamon destroys MetalSeadramon using his own "River of Power". Whamon is destroyed.  It isn't long after that Puppetmon comes up with an evil plan to destroy the kids. He makes dolls of each of the kids and uses these to make them do what he wants them to. He then separates Matt and T.K. from everyone else. Kiwimon attacks the other kids while Puppetmon corners T.K. T.K. realizes what the dolls are used for and tricks Puppetmon and destroys the dolls. The Digimon easily defeat Kiwimon and Puppetmon says that no matter what it takes he will get revenge on T.K. Matt thinks that T.K. no longer needs him around, so he goes off somewhere by himself.

Just when it looks like it is about over for the kids and their digimon, Whamon shows up to rescue them. Soon after their escape, the Divermon are sent out to look for them. While checking over his computer, Izzy discovers that WarGreymon has the ability to destroy Dramon type Digimon. The Divermon find the kids and attack Whamon, but when Whamon dives down quickly, the Divermon can't follow him because they can't handle the pressure change. Izzy uses his computer to find a tunnel that leads to a safe place...for a while that is. Soon MetalSeadramon finds them and Whamon rushes to the surface and ends up in a bay. When MetalSeadramon attacks, Agumon and WarGreymon WarpDigivolve and prepare for battle.

While trying to save the digidestined from Piedmon, Piximon is destroyed. The kids suddenly find themselves back in the DigiWorld, on the edge of the beach. They soon realize that this is the same spot where they spent their first night in the DigiWorld. Shellmon suddenly attacks them, but the digimon quickly take care of the problem. MetalSeadramon sends Scorpiomon after them. Scorpiomon traps the kids in a building where he almost barbecues the kids. They are only saved when Togemon and Ikkakumon digivolve into mega. The kids then hurry to get away, but get trapped in the middle of the ocean.

The kids and their Digimon find themselves back in the Digiworld. Shortly after coming back, Kari finds Chuumon, a mouse-like digimon, who tells them that a lot of time has passed since they left and now the four Dark Masters have moved the DigiWorld to Spiral Mountain and are planning to take it over. MetalSeadramon shows up but the kids and Digimon are able to escape, they are unable to defeat him because he is an untimate level Digimon. The next Dark Master, Puppetmon, controls the kids and Digimon with strings and drops them off to see the fourth Dark Master, Piedmon. Piximon shows up at the last second and rescues them. The third Dark Master is Unknown at this time.

Agumon and Gabumon warp-digivolve into WarGreymon and MetalGarurumon. Even these two ultimate level digimon can't defeat the more powerful than ever, VenomMyotismon. The digimon combine their attacks and the kids crests begin to glow, destroying VenomMyotismon. Just when the kids think their job is finished, they look up into the sky and see that the digiworld is up above them and up-side-down. They then realize that they must fix things in the DigitalWorld before things in the real world will return to normal. The kids make the hard decision to say goodbye to their parents. A rainbow then appears and pulls them back into the sky which is the Digital World.