Headed up by Gumpei Yokoi, the division also created and developed for the Game Boy. In 1986, members of R&D1; formed Intelligent Systems. Whereas R&D1; (which later merged into EAD) concentrated on Game Boy development, Intelligent Systems went on to create such Super Famicom (SNES) hits as Fire Emblem and Super Metroid.

During the SNES days, Intelligent Systems was internally split into different teams: Team Deer Force, responsible for Super Metroid, Team Battle Clash (Super Scope Titles), Team Emblem (Fire Emblem) and Team Shikamaru (Mario Paint).

After working on Paper Mario (N64), Intelligent Systems shifted focus to Game Boy Advance and GameCube development.