A ten-year old boy named Takato Matsuda made up his own Digimon, based on Agumon that he named Guilmon - but one day his card reader mysteriously changed into on odd device - a D-Arc - and the notepaper his Digimon was on was scanned. The D-Arc pointed him to a location where Guilmon had become real. Guilmon's mentality was that off a small child, so Takato had no problems controlling him and brought him home - disguised, of course. Meanwhile, Ruki Makino recieved her D-Arc and Digimon, Renamon, after beating a card tournament, after which she proceeded to delete any Digimon emerging into the real world, believing them to be "only data". Jenrya Lee, after recieving a Digimon game for Christmas, witness a Terriermon emerging from the game and his card reader transforming into a D-Arc. These were to be the three main Digimon Tamers.
Jenrya and Takato soon met and became friends, while Ruki remained apart, battling more and more Digimon. Guilmon and Renamon eventually became engaged in battle, and so Terriermon evolved to Galgomon to stop them. However, his evolution was unstable without the aid of Culumon, and he was essentially drunk on his power, but fortunately, no one was hurt. Soon after, Renamon and Ruki were fighting a Dokugumon against which it seemed winning was impossible - but Ruki realised that Renamon, nor any other Digimon was data, and Renamon evolved into Kyuubimon, who easily defeated Dokugumon. From the beginning however, a mysterious organisation called HYPNOS was tracking the "Wild Ones" - the Digimon emerging into the real world - and the Tamers. They had sufficient technology to delete some Digimon with "Yuggoth", and they captured those they could to experiment. Soon after, when a Devidramon burst through the Digital World/Real World barrier, enraged by the taunting of Impmon, he terrorised humans and ripped several things apart, giving HYPNOS a hard time, for they also covered the existence of Digimon up. The Tamers were also unable to stop Devidramon until Guilmon evolved into Growmon.
After another influx of Wild Ones, and emotinal/mental problems of Ruki, HYPNOS was at last ready to activate Shaggai, the program that was supposed to delete all Digimon. Guilmon, Renamon, and Terriermon were attracted to it, leading the Tamers to the HYPNOS towers. Although many Digimon were sucked into the vortex, as should have happened, an extremely powerful Digimon - Perfect level, higher level than Yamaki and the others at HYPNOS had previously encountered - reversed the vortex, opening a gate between the worlds through which it came. Galgomon and Kyuubimon were both defeated by Mahiramon, the first of the Devas, but when Growmon went to fight he was able to evolve into Megalo Growmon and defeat him.
As it turned out, Jenrya's father was part of the Wild Bunch, the group that had first created the AI that eventually became Digimon in the Tamers world. Due to lack of funding, they had had to give up the project, but one of them, code-named "Shibumi" had continued the project. Somehow, Digimon had found their way to the space created by ENIAC and Atanasoff, where they had grown and evolved. Some of the Digimon had quickly attained the highest level, Final, and claimed the title of gods. These were Qinglongmon, Zhuqiaomon, Baihumon, and Xuanwumon, the four Holy Beasts. An old program called the "D-Reaper" had attacked the Tamers Digital World, wreaking mass destruction, but it disappeared. Qinglongmon sealed the power of evolution into a Digimon - Culumon - and sent him to to real world, so that the D-Reaper would not return because the Digimon exceeded their allocated data size.
Eventually more Devas, in truth the servants of Zhuqiaomon, came to seek the power of evolution, torturing some fleshies along the way of course. One of them, Indramon, proceeded to beat up a frustrated Impmon, where he would lie until Chatsuramon came and allowed him to evolve into Beezlebumon, in return for killing the Tamers. Eventually, one of the Devas, Makuramon, succeeded in this mission, and returned to the Digital World even as Juri, one of Takato's classmates, became the Tamer of Leomon. The Tamers resolved to go to the Digital World to rescue Culumon, and after many adventures, where Hirokazu became the Tamer of Guardromon and they met Ryo Akiyama, the Legenday Tamer of Cyber Dramon, they ran into Beezlebumon, who killed Leomon. A furious Takato forced Megalo Growmon to evolve into Megidramon, the most unstable of the Four Great Dragons, but Beezlebumon was able to overcome him by absorbing the data of Makuramon and part of Rapidmon and Taomon, the Perfect forms of Terriermon and Renamon.
However, Megidramon devolved, and Guilmon and Takato Matrix Evolved into Dukemon, and were able to defeat Beezlebumon, who's life was saved by Juri, of all people. The Tamer went to fight Zhuqiaomon, who they found wasn't the real enemy. Qinglongmon, Zhuqiaomon, and Shibumi told them the history of the Digital World and that the D-Reaper was the true enemy. Culumon released his powers so all the Digimon in the Digital World could evolve to Final and help fight against the D-Reaper, while the Tamers were sent back to the Real World, as were Culumon and the humiliated Impmon. However, the D-Reaper was in the real world as well, so the Holy Beasts sent them aid in the form of a Dobermon, which transformed the Tamers back into data, allowing them to Matrix Evolve. Dobermon died doing this, and a mysterious girl named Alice who traveled with him disappeared as well . . .
However, the "Juri" that was with the Tamers turned out to be the Agent of D-Reaper 01, and the real Juri was trapped within the D-Reaper. After several battles, and the shiny heroic of Beezlebumon Blast Mode, it seemed they had failed. However, at last, Dukemon Crimson Mode was able to save Juri as Saint Galgomon executed Shaggai, which devolved the D-Reaper into a harmless state. However, to keep the real world secure, the Digimon had to leave. Even though they felt they would see their Digimon again, they were sad . . .except for one.