The "Dark Ignis" (闇やみのイグニス, Yami no Igunisu), alternatively named Ai, is the deuteragonist in the first and second seasons

Ai was created by Dr. Kogami, the scientist who created the Ignis. The Ignis were developed by watching the six test subjects Duel, with Ai modeled after Yusaku Fujiki. Eventually, Ai and the other Ignis evolved and created the Cyberse World, as well as the Cyberse monsters.

Their progress worried Dr. Kogami who created Ignis to help humanity, and predicted through his simulations that the AI and humanity would become enemies.

Despite this, Ai and the other Ignis continued to create their world, each with a sector based on themselves. In Ai's words, the Ignis would never try to harm humanity, and would rather live in their own world

(Source: Yu-Gi-Oh! Wikia)