There may have originally been an extra planet, which lost its spot, burst through the asteroid belt, causing many asteroids to scatter and bombard other planets (and our moon).

Astronomy.com reports:

"...a body with about half the mass of Mars, originally located about 1.9 AU from the sun, and with an orbital inclination of zero. The planet would slowly be nudged by the other planets into an eccentric orbit which had the planet cross the asteroid belt and then fall into the sun about 600 million years after its creation."

It appears that they just ran computer models for ages until something fitted. They seem to have shown that it could of happened, but won't be able to prove that it definitely did.