The sequel takes the original game's formula of a little ship with big weapons amidst tons of glowy balls, but adds two-player co-operative multi-card play, in addition to single-card duels. The game also features horizontally scrolling levels a la Gradius to complement its vertically scrolling top-down stages.

Nanostray 2 makes use of Nintendo's Wi-Fi Connection, but this is unfortunately only used for online leaderboards and not multiplayer battling or cooperative play. Prior to its work on the Nanostray series, developer Shin'en created the Iridion series of graphically impressive shooters for the Game Boy Advance.