All characters:
At the title screen, hold White + Black and press Up, Right, Left, Down. Release White + Black then press L + R.
Through The Portal bonus mission:
At the title screen, press White, Up, Black, Down, L, R, Left.
B-side commentary:
At the title screen, press hold L + R and press Down, X, X, Up, X, X, Left, X, X, Right, X, X.
All story mode missions:
At the mission select screen, press White, White, L, R, Right, X, L3, R3.
All layouts:
At the mission select screen, press R3, L3, L, R, White, Black.
All ninja items:
At the item selection screen, hold L + R and press Up, Down, Up, Down, X, X, X, Left, Right, Left, Right, X, X, X.
Increased ninja items amount:
At the item selection screen, hold L + R and press Up, Left, Down, Right, X, X, X.
Unlimited item capacity:
At the item selection screen, hold L + R + White and press Up, Up, Down, Down, Left, Right, Left, Right. Release White and press X, X, X.
Restore health:
While playing, press pause then press Up, Down, Up, Down, X, X, X.
New special move:
While playing, press pause then hold R + Black and press Up, Up, Down, Down. Release R + Black and press X, X, L, R.
Increase Kuji by one:
While playing, press pause then press Left, Left, Left, Right, X.
Full Kuji:
While playing, press pause then hold L + R and press Left, Left, Left, Right, X.
Display score:
While playing, press pause then press Right, Right, Right, Left.
Increase score:
While playing, press pause then press hold White + Black and press Right, Right, Right, Left.
Increased offensive power:
While playing, press pause then hold R + White and press Up, Down, Up, Down. Release R + White and press X, X, X.
