Most of the gameplay focuses on finding clues and battling Noise. Battles consist of player-chosen encounters. The player may scan the area for fights at any time. The game also features a very flexible difficulty curve. Players can influence item drop rates by altering the game's difficulty and the player's current level. Players can use Neku's mindreading abilities to hear people's thoughts by using the touch screen of the Nintendo DS. The game's combat system, called the "Stride Cross Battle System", uses both screens of the Nintendo DS. Neku has one of three partners, different in each chapter of the game. The player can freely choose which partner to use once clearing the game. The partner is displayed on the top screen, while Neku is displayed on the bottom. Battle actions take place simultaneously between both characters. The touch screen is used to move and attack with Neku, whose abilities depend on the pins equipped. On the top screen, movement can be controlled with the D-pad, which is also tapped for specific techniques.The game is divided into three chapters, "Shiki Chapter", "Joshua Chapter", and "Beat Chapter". An extra story, "Another Day — It's a Wonderful Day", Anazā Dei, is accessible after clearing the main game and fulfilling every day's reports. A pin collection system allows players to use new abilities by collecting pins scattered throughout Shibuya, obtainable either through defeating Noise or purchasing them in stores. Different pins allow Neku to use a variety of abilities. Players can buy clothing and food for Neku and his partners in the stores located all across Shibuya, to increase their Brave points, offense and defense points, or synchronization percentage.
HP between Neku and his partner is shared, and when Neku and his partner lose all their HP during battle, the game is over. The player is taken to a selection screen to choose an action: retry the battle, retry the battle on Easy Mode, flee from battle (unavailable for key boss battles and when black Noise symbols are chosen for battle), or return to the title screen.
Players can also play a mini-game named Tin Pin Slammer, a game similar to the Western marble game ringer. This is played by dragging and clashing pins to knock off the opponent's pin off of the arena. Each pin has a different weight and special attacks.
