General Pepper has fallen ill, and requests that (the now elderly) Peppy Hare take his place. Meanwhile it is discovered that Venom has acid oceans, which are home to the dangerous Anglars. Now the team must save the Lylat system again!
The single player mode is split into thirty map-based combat and Battle combat missions. During map mode you control your Arwings with the stylus. During combat, you move your Arwing by sliding your stylus to the left/right. Bombs are controlled with the touch screen. You may fire the cannons with any button but Start/Select.
Star Fox Command's six-player Wi-Fi mode plays like the Shine Runner mode from Mario Kart DS and the Star Fox 64 multiplayer game. You shoot your friends down for stars.
Star Fox Command has new pilots (Octoman is one of the CPU pilots) and ships, multiple endings, and a new gibberish generator (make your own pilot noises). It also has support for the brand new DS rumble pak.
In the opening of this game, a picture of the puppet-like versions of the four original members seen in the first Star Fox is shown (even though the first game doesn't fit into the current Star Fox continuity).