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.

Alternate title screen colors:
Press Left or Right to get different colors at the title screen.

Ninja mode:
The ninja's face is in the background at the title screen . Play close attention and observe his mask.Watch as it goes away revealing his face. As soon as this happens, press Start and you will be able to play as Ninja from the beginning of the game. A sound will confirm correct code entry in some versions of the game.

Get your accomplishment rate up to at least 85%.

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.

Hint: 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.