Star Fox: Assault's development began with its Battle Mode, which explains why it was the first and only feature shown off at its E3 2003 showing. The battle mode in Star Fox 64 was merely just a last-minute bonus, so Takaya Imamura had desired to create a more fleshed out version in a future Star Fox title. This is where Namco handed Nintendo a couple of design documents patented as "Vehicle-Swapping War Action Game", and that's what would be the starting point for Assault's development.

It seems that work on the single-player mode didn't really begin until midway into development. Apparently, as the development team had focused so much of their energy into Star Fox: Assault's battle mode, there were serious talks to abandon the single-player aspect entirely and just make the title a pure multiplayer game. Of course, the development team recognized that many fans would wanted a proper story mode, so they pushed forward on it. Assault's director Toshiyuki Nakanishi explains that this is why the game had a lengthy development cycle.