Guilty Gear Petit 2 is very similar to its predecessor, Guilty Gear Petit for the same platform, having the same "super-deformed" graphical style, battle moves (including the tension system to accumulate power and combo attacks), as well as backgrounds for battles. Several new characters appear in Guilty Gear Petit 2, such as Zato-1, the former head of the assassin guild, the pirate captain Johnny, and others.

Ky Kiske returns to defeat all the opponents with his Destroy Move and finish the game even faster than the previous run, mostly thanks to only doing one round per match.