Technology, science, and industry—this is 1969 Tokyo, and there is no better time to be alive! But a shadow looms quietly around every corner: "Invaders" have infiltrated the populace, and nobody knows who or what they are. Only the members of the top-secret agency AEGIS know of their existence. Covertly fighting the enemy is their job, but only those with the ability to open "Gates" to another world can truly defeat them. Within AEGIS is a specialized task force known as the "Gate Keepers." Composed of extraordinary individuals with a variety of Gate-related abilities, they are the only ones who can save humanity from the vicious Invaders plaguing the planet. Shun Ukiya is an average high school student who lives with his widowed mother and little sister. While on his way home from school one day, he comes across a group of Invaders heading toward his house. In a desperate plight to save his family, Shun discovers he possesses the ability to open a Gate, allowing him to harness massive amounts of energy. With his newfound ability exposed, he catches the attention of AEGIS, and particularly the interest of one of its Gate Keepers, Shun's childhood friend Ruriko Ikusawa. [Written by MAL Rewrite]

The story takes place on an island, where a "Fractale System" is beginning to collapse. One day, Clain finds an injured girl called Phryne under a cliff. She disappears leaving a pendant. Clain sets out for a journey with the girl-shaped avatar Nessa to look for Phryne and discovers the secret of the Fractale System.

Upon meeting for the first time, undefeated street fighter Marcus Damon and renegade Digimon Agumon become friends in the most natural way possible for the knuckleheaded duo—by fighting their hearts out. The self-proclaimed "ultimate team" are recruited by a secret government organization called the Digimon Data Squad, or DATS, who had witnessed an unbelievable human fighting blow for blow with a Digimon. Their primary objective is investigating mysterious problems caused by Digimon entering the real world, and the world is currently in the midst of a crisis with Digimon appearing at an unprecedented rate. Embarking on various missions with DATS, Marcus and Agumon become colleagues with adolescent genius Thomas H. Norstein and his Digimon partner Gaoman, along with the kind-hearted Yoshino "Yoshi" Fujeda and her Digimon partner Lalamon. As the group continues to investigate the rapid increase of Digimon in their world, a darker truth begins to surface, and it is up to Marcus, Agumon, and their friends to get to the bottom of things. [Written by MAL Rewrite]

In the year 2020, technology is everywhere. Every digital device around the world is connected by a singular network where data travels. Unbeknownst to humans, this network has become home to life forms known as "Digimon." Fifth-grader Taichi Yagami is preparing for summer camp when strange occurrences begin in Tokyo; certain electronic systems have started going haywire. When he discovers that his sister and mother are trapped on an unstoppable train, he rushes to the nearby station. Suddenly, Taichi is transported to another world where he meets a strange creature by the name of Agumon, who somehow already knows his name. Taichi also receives a strange device called a "Digivice," which allows him to communicate with the undigitized world. Taichi discovers he is in the "Network," and virus-like Digimon are attacking the areas that maintain Tokyo’s electronic systems. It is up to Taichi and his new partner Agumon to stop these cyberattacks before the whole world is threatened by the actions of mischievous Digimon.