The game starts with a Ninja in training (simply named Ninja), who comes to rescue his Sensei (simply named Sensei) from the Ranx sent by Ninja's nemesis, Emperor O-Dor. Ninja saves Sensei by defeating the Ranx. Then, a creature comes to attack Ninja which he deals with easily. The creature then spits out a Rage Stone which Ninja touches and goes into a fit of rage and accidentally kills Sensei. Sensei comes back as a ghost and tells Ninja that there are more Rage Stones and with their power, he can defeat O-Dor. Sensei then sends Ninja to find the second Rage Stone in Robot Beach. Ninja then arrives at Robot Beach.
The main character in I-Ninja has a variety of acrobatic abilities that are used throughout the game to defeat the Ranx army led by Master O-Dor. In addition to basic skills such as running and jumping, Ninja can also double jump, spin his sword around while midair for a limited time and use it to fall slower than normal, and use the shape of the environment to his advantage. Throughout the game there are several uniquely designed walls that Ninja can run on, and points where Ninja can use his grappling hook to swing across a gap.
Certain levels also provide Ninja with explosive darts and ricocheting shuriken to use against his foes; both of these can be aimed using a first-person view, but shuriken can also be thrown with an auto-aim feature. Occasionally, Ninja will encounter an enemy that will leap into the air with him (in anime fashion) to battle, and the two will remain suspended in a sort of flying void until the foe is defeated. While in this void, Ninja flies around and can dash, slash with his sword, perform an unblockable but heavily delayed thrusting attack, and throw shuriken if he has them. As Ninja attacks he will build an attack gauge that, when filled to certain levels, can be spent to temporarily enhance his abilities.
As the player progresses through the game he will gain access to more of these abilities; using them he can increase his strength, heal his life bar, ride a giant shuriken to quickly slay foes, or even become invincible, which allows him to greatly harm enemies in his vicinity without even touching them. (When Ninja becomes invincible, he says "I-Ninja!", which provides the game with its namesake.)
I-Ninja was generally well received among critics and gamers alike, on Metacritic, I-Ninja has received zero negative reviews and has more positive than mixed and received 73/100 overall.
IGN said "I-Ninja packs so much personality and attitude into its formulaic design that its charm and personality lift it above the fray of me-too titles" GameSpot reviewer Ryan Davis said "At first glance, I-Ninja may appear to be a simple action game designed for kids, but in reality, it is anything but. The visual style may seem kid-friendly, but the level of challenge I-Ninja has to offer keeps the game interesting for a wider audience".
The game's protagonist has been included on the lists of video gaming's top 10 ninja characters by 1UP.com in 2004 and PC World in 2010.