N3: Ninety-Nine Nights is the story of the War with No Name, a large scale battle between the forces of dark and forces of light. Initially the many different races of the world lived in peace, a power granted by mythical orb which created the world. However, the orb is mysteriously shattered which leads the different races (humans, elves, orcs, goblins, and more) to distrust each other and eventually leads to the giant, unnamed battle. Throughout the game you control seven different characters, each of which provide a different perspective on the battle. Some parts of each characters story overlap allowing a different point of view while other parts are unique. Initially only one character is available, and by progressing through the game the additional characters will be unlocked; in order to see the complete story you will need to complete all of the scenarios for each character.

Each scenario in the game is a large scale battle involving hundreds of opponents to defeat; each character you control has a variety of moves available and as you level up additional moves become available. The varying maneuvers available are performed by pressing different button combos on the controller. As you defeat enemies red orb crystals are earned which fill a meter; when the orb meter is finally full you are able to perform a more powerful attack capable of taking out many foes. While performing this attack you earn blue orb crystals which fill up a second meter; when that meter is full you have one of your most powerful attacks available to you.

Since you will be fighting a significant number of enemies at one time you don't enter battle alone; two groups of warrior guard units fight with you. At the beginning of each mission you can choose the type of guard units to bring with you, such as archers who specialize in long range attacks or the infantry who are better at close range combat. You also have the ability to give them some simple commands such as calling the guards to your side for protection or attacking a target.

As you progress through the missions, different items can be found. These include more powerful weapons, improved armor, or magical items which increase your hit points or decrease damage received. After each mission a new mission will become available on the world map; you have the option of playing or replaying any of the missions which are unlocked on the map which allows you to level up on easier missions if you have trouble defeating one of the tougher ones.