Naruto: Ninja Council

Beat the game once.

Beat the night missions with all 3 characters, collect all 100 Leaf symbols.

Red - Preforms Chidori, hits all enemies on screen.
Yellow - More powerful version of red jutsu.

Beat the game with Naruto and Sasuke.

Red - Uses Kyuubi to heal himself.
Yellow - Uses Kyuubi to heal himself, then deals damage to all enemies on screen.

Red - Preforms an upward kick-aerial combo.
Yellow - More powerful version of the red combo.

On the Leaf Village Arena level, 1st Area (first level where you get the wind scroll) near the end of the level, you will fight a jounin-level enemy (big green ninja) and to the right of the platform he is standing on, there is a small crawl-way. Inside of the room, there is a large invisible scroll. When you acquire it, that character will permanatly learn level 4 Jutsus (if you save your game.)

Collect all 100 Leaf symbols.

Use Naruto's Naruto Rendan (3rd special) in the red part (causing him to fail) against Kiba. Naruto will fart and cause Kiba to be paralyzed then Naruto will finish it up with Naruto Rendan.