Similarly to the origins of HAL Laboratory, the team soon became an auxiliary program unit for Nintendo that provided system tools and hired people to program, fix, or port Nintendo-developed software.

[5] Narihiro programmed his first video games, Famicom Wars and Fire Emblem: Shadow Dragon and the Blade of Light, towards the end of the Famicom's life cycle, although the game design, graphic design, and music was provided by the Nintendo R&D1 team.

The company continued to develop new entries in the Wars and Fire Emblem franchises.

In 2000, Intelligent Systems produced Paper Mario for the Nintendo 64, which became a surprise hit, leading to five sequels.

Cubivore: Survival of the Fittest (which was co-developed by Intelligent Systems) was published by Atlus in North America; Intelligent Systems also developed various Dragon Quest games, which were published by Square Enix.