After the end credits, there are two revealing phone calls by Ocelot.
The title sequence doesn't appear at the beginning of the game - it appears when the Virtuous Mission ends (which is well into the game). If you save anytime after this point, the sequence will appear at the beginning the next time you play.
The title sequence is interactive. The player can make the credits move like a snake and change them into snake skeletons and into a number of languages. They can also overlap the sequence with different symbols, including peace signs, flying geese, fighter jets and parachuting soldiers.
Before the credits roll a time-line is shown detailing events that follow the game, including the US branch of the Philosophers renaming itself "the Patriots," the founding of FOX-HOUND, and the Les Enfants Terribles Project.