Nicholas Flamel, creator of the Philosopher's Stone who kept it safe for five centuries, was remarkably cooperative when Albus Dumbledore said to him, "That British dark wizard who died ten years ago is after it, I think you should give it to me to protect."

He was even more cooperative when, after all the trouble they'd gone through to protect it, Dumbledore suggested it be destroyed.

The Carnivorous Muffin and Vinelle have a theory: Nicholas Flamel is dead at the beginning of the book, and Dumbledore took the Stone.