According to what I was taught in science class, the Y chromosome is simply an X chromosome that has undergone no fewer than 4 inversion mutations. In an inversion mutation, parts separate and, well, invert themselves, then reattach. In an inversion mutation, often sections are lost due to the breaking. This eventually, over thousands and thousands of years, resulted in over 100 million base pairs being lost from the Y chromosome.
That is, if I remember correctly. And I think I do.