Takato Matsuda, Ruki Matsuno, and Lee Jenrya are children who have, by fate, recieved real Digimon, unlike the imaginary ones in the card game they play. Each of the children, or "Digimon Tamers", have their different views on how Digimon should be treated. But when other Digimon begin to appear around Japan, they must put aside their differences to fend off the digital intruders; even though Yamaki, who is the head of a secret organization called Hypnos is trying to eliminate all of the Digimon himself.
In their closed-off underground village, Kamina and Simon chafe at the limits imposed by the village elder. Yet all this will change, when Simon stumbles across a fantastic device—just as the village's peace is broken by a violent intrusion.
Lain Iwakura appears to be an ordinary girl, with almost no experience with computers. Yet the sudden suicide of a schoolmate, and a number of strange occurrences, conspire to pull Lain into the world of the Wired, where she gradually learns that nothing is what it seems to be... not even Lain herself.