To get the Ninga suit -- you don't have to beat the game 4 times, just 3. here's how:

1. Resist to Ocalot's torture chamber, and beat the game. Meryl will give you a bandana (unlimited ammo), then save your game. [NOTE: Make sure you overwrite your saved games so they'll be on the same memory block]

2. Submit to the torture and beat the game. Otacon will give you his stealth suit (invisable suit), then save your game.

3. Now load your saved game [you should have a ninja icon stored in your memory block] and you will start at the Docks. Now here's the tricky part: Don't use your bandana or your stealth suit, or you won't get the ninja suit.

Instead; After you beat Ninja the story-line will change and you'll have yourself a nifty ninja suit.