Alternate Costume:
Complete the game on normal or hard difficulty. Then hold L while selecting the "New Game" option at the opening menu to wear the Ninja Of The Future costume.
Plasma Saber:
Complete the game on normal difficulty. A new sword called the Plasma Saber will be unlocked.
Skip FMV Sequences:
Press Start, A, Start to skip a FMV sequence.
All FMV Sequences:
Complete the game on normal or hard difficulty to unlock all FMV sequences.
Very Hard Difficulty:
Complete the game on normal or hard difficulty to unlock the very hard difficulty setting.
Unlock Classic Ninja Gaiden:
Give 50 Scarabs to Muramasa. This does not have to be done in a single game play-through. You can continue from a completed game save and collect the Scarabs that were originally missed until you have the required 50 Scarabs. After giving them to Muramasa, you will get the Ninja Gaiden disc to be used at the arcade machine at Han's Bar's first floor.
Unlock Classic Ninja Gaiden 2: The Dark Sword of Chaos:
Get a "Master Ninja" rank in all levels under the normal difficulty setting.
Alternately, first unlock Ninja Gaiden. Then go to the Clock Tower Plaza of Tairon. Get on the ledge above the multicolored door that leads to Pleasure Street (where you flip the switch to unlock that door). Aim your bow at the clock tower across the street. Shoot the face of the clock and a treasure chest will appear on the building that is across the street. Jump down, and enter the doorway across the street with the stairs. Climb to the top, and open the chest to unlock the Ninja Gaiden 2 disc.
Unlock Classic Ninja Gaiden 3: The Ancient Ship of Doom:
Get a "Master Ninja" rank in all levels under the hard or very hard difficulty settings.
Alternately, first unlock Ninja Gaiden 2. Go to the Peristyle Passage (the ceremonial room in the Aqueducts, just before the Boss fight with the giant fossil bird). It is next to the Hall of Balance. Triangle Jump back up to the top of the broken pillar where a Scarab was previously hidden. You will now find the disc for Ninja Gaiden 3 at that location.
Unlock Classic Ninja Gaiden Games:
Instead of going to the first floor of Han's Bar, use the following trick to start the games from the main menu. Successfully complete the main game while any classic Ninja Gaiden disc is in Ryu's inventory. This will unlock another main menu option that will allow you to play the classic games from there, without going to Han's Bar.
Classic Ninja Gaiden Passwords:
Level Password
1 L, X, A, Y, A, X
2 A, X, X, R, Y, A
3 X, Y, B, R, L, X
4 B, R, A, B, Y, Y
5 X, A, Y, X, L, L
6 R, Y, R, L, A, X
Classic Ninja Gaiden 2 Passwords:
Level Password
1 A, A, B, X, Y, R
2 X, L, R, B, B, A
3 L, Y, B, A, R, R
4 A, L, X, Y, Y, B
5 R, A, A, B, X, L
6 Y, L, R, A, Y, R
7 B, B, X, Y, A, L
Classic Ninja Gaiden 3 Passwords:
Level Password
1 B, Y, R, L, X, A
2 B, Y, R, L, X, A
3 L, B, R, Y, L, Y
4 R, R, B, A, Y, X
5 Y, A, B, X, R, X
6 B, X, X, A, X, Y
7 X, R, X, Y, Y, L