Your description, changing a few particulars, sounds like "Dormant", by A. E. van Vogt, which first appeared in the November 1948 issue of Startling Stories.
The monster of the story was named Iilah. Iilah was a robotic weapon that came to Earth during a prehistoric alien war, and was deactivated by an enemy weapon. Iilah was four hundred feet long and one hundred feet wide, and to humans looked like a two-million ton rock. (The first Americans to arrive at the island are puzzled to find the giant rock atop the island's mountain, as such a rock did not appear in their reconnaissance photos.) Iilah lay in the lagoon of a Pacific island for millions of years, until fallout from the early atomic weapons woke it into an amnesiac state - the monster knows it's supposed to do something, but can't remember what. Iilah cannot see water, so when an America navy ship arrives at the island after World War II, the monster perceives the ship as levitating. Iilah assumes the ship to be some type of being. Iilah's attempts at communicating with the ship kills many crewmen with hard radiation. When the ship fires back with cannons, Iilah first assumes the attack to be an attempt at communication, but the damage the monster receives changes its mind and it moves into the water and rams the ship onto the beach. Iilah then goes on a rampage across the island, killing hundreds of men - but their deaths were not intentional. Iilah did not even know that the men existed as human bodies were invisible to the monster, being mostly water. As a last resort the military decided to kill the monster with a nuclear weapon; as the bomber approached, Iilah sensed the weapon as something like itself. The explosion provided Iilah with enough energy to overcome his amnesia and recall his purpose on Earth. The monster did not then depart, but destroyed the Earth. The story's final line reads, 'Even if Iilah had known that it was not the same war that had raged ten thousand million centuries before, he would have had no choice but to do as he did. Robot atom bombs do not make up their own minds.'
