"When a particularly loud crack of "thunder" was heard, it was thought that something more than mere lightning had buried itself in the ground.. Certain unusual objects found in the earth were popularly called "thunderbolts" or "thunderstones" including fossil belemnites, sea-urchins, quartz crystals, iron pyrites and stone axes...On the principle that lightning never strikes the same place twice, such objects were valued and sold on as protectors against lightning strikes."
Oxford Dictionary of Engish Folklore

In this particular case, the stone was probably seen as a very large thunder bolt. Any evidence of bits being hacked off as protecting charms?