Gennai serves as a guide to the Digital World. He is a mysterious being that the DigiDestined first encounter after the battle with Devimon. He claims to be data, but without the same attributes as Digimon. Gennai appeared first to the DigiDestined as a very old man, but when Kari is possessed by the powers of light and gives them a glimpse of the history of the Digital World, he is seen as a young man wearing a hooded robe that somewhat resembles clothes of a Jedi Knight, apparently one among many of his kind. Gennai and his group were the ones that created the Digivices, Tags, and Crests, as well as choosing the Chosen Digimon.

Soon, however, the Dark Masters discovered their plans, and Piedmon, along with an army of Guardromon and Mekanorimon, invaded and destroyed the secret base, killing all save Gennai. Piedmon stole the Tags and Crests, but Gennai interrupted him by attacking him with a sword. Piedmon inserted a mysterious black ball into Gennai before Gennai leapt into a Mekanorimon and kicked the Bakemon driver out—escaping with the Digi-Eggs of the Chosen Digimon and the Digivices. In the process, he dropped one egg — Gatomon's — which later hatched and grew up alone. The purpose of the mysterious black ball was never officially explained on screen or by any members of the series' production staff. Many fans believe that it caused Gennai to age into the old man he was in the first series.

Later, Gennai's secret base became Myotismon's castle.

At some point after Digimon Adventure, Gennai called the DigiDestined back into the Digital World to ask them to give up the power of their Crests to add another layer of protection to the Digital World, which they did. He did not appear again until the second series, where he appeared as a young man. It is thought that he accomplished this by copying himself, as many more of his kind later appeared in the series, and one of them stated that he and Gennai were once one and the same. It is possible that the people seen with him in the flashback in the first series were also copies of the original Gennai.