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!!!

The DigiDestined see that Ken's base is about to explode. Okuwamon, a digimon made from control spires, attacks the DigiDestined. Ken comes, and Davis talks about friendship. Suddenly, ExVeemon and Stingmon DNA digivolve to Paildramon.

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.

The strange woman changes control spires into digimon. She turns one into a Golemon who tries to destroy a dam where Mimi and Palmon are. The DigiDestined cannot destroy Golemon and are forced to get Ken and Stingmon's help to destroy Golemon. Once Palmon wakes up and reveals that Golemon is a fake digimon, which is deduced as the reason behind Ken's actions, Yolei is able to get Hawkmon to digivolve into Aquilamon and helps destroy Golemon.

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.

Davis, Kari, and T.K. find that their Digimon can't Digivolve. Cody is attacked by Thundermon, leading to Armadillomon's unexpected digivolution into Ankylomon. Ken sees a strange woman in his room that won't tell him her name. When a mysterious digimon who is Stingmon, Wormmon's evolved form destroys Thundermon, it leads the DigiDestined to question Ken's behavior.

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.

Ken reminisces about his brother Sam, his digivice, an e-mail he got, and when he first went into the Digital World (despite his temporary amnesia in the real world). He goes looking for Wormmon, and finds his baby form, Leafmon, in Primary Village.

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.

Davis, in an effort to catch Kari's attention, wants Veemon to evolve like Patamon. His effort only manages to anger a Tortomon that chases them across the land. Veemon digivolves to ExVeemon to fight him off.

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.

Kimeramon and Magnamon fight. Ken's base explodes, and Wormmon gives all the power he has to help Magnamon defeat Kimeramon. Kimeramon dies, and Ken gets upset because Wormmon is dead like his older brother, Sam. Davis finds the Crest of Kindness on the ground and gives it to Ken.

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.

Kimeramon soundly defeats the DigiDestined. Wormmon leads Davis and Veemon to the power source of the base. It turns out to be a golden Digi-egg, which Davis uses to golden armor digivolve Veemon to Magnamon.

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.

All of the new DigiDestined (except Davis, who can't fly to the location) sneak into Ken's base. Ken goes into the Dark Whirlpool, even through Wormmon told him not to. Devimon comes out, and T.K. gets mad because of what he did to Patamon long ago and fights Ken. When Ken escapes T.K., he releases Kimeramon on the DigiDestined, and they must flee.