Play as the Ninja
During the intro movie, it'll show the title screen a few times and the Ninja with his mask closed. Wait for it to cycle about three times. The fourth time, the Ninja's mask will be open, press start at that instant. The title screen will have his mask open. You can then select the Ninja option from the Special category.

Alternate selection screen:
Press Start at the Konami logo before the introduction to the game in order to get a different picture at the selection screen. Instead of a pictures of the Ninja, it will feature the Ninja with his mask broken open.

Mei Ling photo session:
Complete sneaking mode with the best time in all thirty time attack levels. An option that allows a photo session with Mei Ling will be unlocked on the "Extras" menu.

Metal Gear Rex preview:
Get to the final mission with at least a 96.6% rating. Complete the final mission to view a screen that features the next Metal Gear model from Metal Gear Solid 2: Sons Of Liberty on the PlayStation2.

Completing Variety Mission 13
Knock down the giant soldier on the right (that enters first), before both of the soldiers get to the point when they stand still. While the first soldier is falling over, the second soldier will reach his post and stand still. The first soldier will get up, become confused, roar, and attack the second soldier. They second guy will get up and fight, finishing the mission for you.

Completing advanced mode level 3 for the Nikita
Go down to the third step from the bottom. Face toward the bottom of the screen and fire. Guide the missile around the outside of the stage and to the back of the stage. Let the missile hit the wall behind the guard. This will kill the enemy and save time on time attack.

Easy record time on ninja level 3
Note: Do this repeatedly until Snake is in the correct location; he may not always be there. As soon as you start, run down the hall without swinging the sword and hang to the left hard. Ignore the guard, as he will not be bothered unless you do not hang to the left. Once past the guard, run to the left, around the corner, and straight to see and kill Solid Snake. Repeat this as many times as needed until Snake is in this position. After he is dead, run straight to the goal and you should have a first place record.

Ninja mode:
Get your accomplishment rate up to at least 85%.

Special mode unlocked
While playing any level on sneaking mode pause the game and hold L1 and press L2, R2, Triangle and R1. Then Unpause the game and keep repeating until you hear Snake say something. Then go to special mode and everything will be unlocked!