This movie is about a U.S. and Japanese joint military experiment that takes place on a small Island off of Japan. The experiment is to test a chemical that can turn salt water into purified water so that it can become a safe drinkable source of water. The experiment is supposed to be carried out on a salt water lake on the Island, but the military is getting a lot of resistance from the Islands natives who claim the military will wake O-baki an ancient monster lives in the lake. O-baki is what they call Varan in the English version of this movie but he is more commonly known has Varan, so I will refer to him as Varan.
Varan is soon spotted at sea and attacks a small fishing boat. The navy and air force begin attacking Varan but all the missiles, bombs, and gun fire appear to have no effect. Varan soon makes land fall and attacks an airport. In a desperation attempt the military attempts to use a highly concentrated version of the chemical they used on the lake to attack Varan. The chemical works and Varan appears to be hurting from it. Varan stumbles into the ocean and dives to the bottom. No one knows if Varan is alive or dead and the movie ends.