The game uses the Wii Remote in unison with the Nunchuk by waving the controller in different directions, but the GameCube controller and the Wii Classic controller can be used with the game as well. Also new to the system are plane switches, where characters after hitting their opponents with a hard flying attack force them out via a cinematic, where they rush after them to a new area of the stage. During this time, the one who sent the foe flying can either chose to do nothing and let them fall to the ground in the new area, teleport behind them to give them even fair ground in landing, attack them or teleport out of sight and behind them in the new area to open them up to combos via a ground bounce from a fall. However, the one sent flying with proper timing in response to the pursuer can counter these actions by dodging or recovering, making it a bit of a Quick-Time Event. This function becomes a mainstay for the whole Wii sub series of the Gekitō Ninja Taisen/Clash of Ninja series.
Also new and part of the mainstay are objects on the arena where characters can move next to in order to hide behind. Doing so they can perform one of their many attacks after slipping out of cover, hop over the object to assault the foe with midair attacks, or simply dodge away from the object. Both players can hide behind the same object, and they can be damaged and broken, leaving the hiding character in a stagger if they are happening to be hiding behind one of them. Characters can also knock each other into the objects with attacks for a "wallbounce" effect seen in more traditional fighters.
The game takes place during the Naruto: Shippūden series, specifically the first ten episodes of the Kazekage Rescue Mission. The game contains re-done Shippūden versions of 12 characters from the previous games in the series and two new characters specifically from the Shippūden series.