Intelligent Systems was founded in February 1984 by Gunpei Yokoi who after working under Shigeru Miyamoto for Nintendo's R&D1 decided that he needed to expand the company and formed Intelligent Systems. During the early years Intelligent System worked along with R&D1 developing games such as Excitebike, Metroid, Ice Climber and Kid Icarus. Intelligent Systems was a nameless company working in background while E&D1 received most of the credit until Paper Mario on the N64 released in 2000.
In 1988 Intelligent Systems released the first Famicom Wars game, which like Fire Emblem, was a Japan only title until the Gameboy Advance where the series was released outside of Japan as Advance Wars.
Two years later the first Fire Emblem game, Fire Emblem: Dark Dragon and the Sword of Light, was released for the Famicom by Team Emblem using the foundations laid down by Famicom Wars, adding RPG elements to the formula and creating the first Strategy RPG (SRPG) as well individual characters instead of generic nameless units as well as adding permanent death to said characters.
The Fire Emblem series was originally created by a name called Shouzo Kaga, however Kaga left the company after Fire Emblem 64 was cancelled and formed his own studio company, Tirnanog.
Intelligent Systems don't just develop software; they also develop hardware such as development tools for Nintendo's consoles as well as tools to capture screenshots of games as well as ROB, the Robotic Operating Buddy used to help market the NES to the US market. Intelligent Systems also created Wario during the Gameboy years for Super Mario Land 2 as an anti-R&D1 design to free IS from R&D1's shadow.
After the Virtual Boy's failure, Gunpei Yokei retired from Intelligent Systems and was replaced by Takehiro Izushi from Intelligent Systems, Team Shikarmaru.
Free of E&D1 Intelligent Systems were able to create games such as Advance Wars, Fire Emblem, Paper Mario and the excellent WarioWare series. Intelligent Systems are currently developing software for the Wii, DS and DSiWare including Bird and Bombs and Dragon Quest Wars co-developed by Square-Enix.