How do I ';clear'; the game in Metal Gear Solid 4? Is that the same as beating it?

Also, I beat the game and saved it, but when I meet up with the MkIII in the first act to recover my saved weapons and DB, it doesn't work... what am I doing wrong?How do I ';clear'; the game in Metal Gear Solid 4? Is that the same as beating it?
You are supposed to reload your saved file from your completed save and you will start a new game over it automatically and should then get your items back.