With their headquarters a shambles after the battle against the Hulk, the Avengers call in a construction crew for repairs. Then, as they depart to attend to their affair, Captain America leaves to teach Rick Jones some acrobatic tricks.
Sometime later, as technicans are assembling an artillery computer at Tony Stark's factory, a piercing sound fills the air and tears the machine apart. The same sound also collapses an anthill that Henry Pym and Janet Van Dyne are exploring and causes other mishaps. Donald Blake goes into action as Thor and soon finds Captain America who is demonstrating his skills to Rick and the Teen Brigade. When a second sound splinters a nearby tree, Thor, Captain America and Rick Jones head for Avengers Mansion. The Avengers soon determine that the source of the sound lies somewhere in the south western United States.
Meanwhile, the soldiers at a secret southwest missile base are surprised to find a large, hill sized rock being thrust up through the ground. As General Ross, the no-nonsense base commander, orders the object's disposal, his daughter Betty arrives with Bruce Banner. Ross berates Banner for abruptly disappearing during a vital atomic test, but Banner pays no attention and thinks only about his experiences since he became the Hulk. He does, however, agree to investigate the growing hill. No one is yet aware that the subterranean Lava Men are responsible for the phenomenon. They are mechanically hoisting the hill at the command of their witch doctor, who wants to conquer the surface people. Only one Lava Man, Molto, realizes the futility of war, but he is silenced and ignored.
Banner soon discovers that the rock is radioactive, and Ross orders it destroyed by missiles. Before they can be fired, the Avengers and Rick arrive, and Iron Man's repulser blasts quickly establish that the rock is not just radioactive but is in some way alive. Iron Man strips off the rock's outer layer, sending shock waves underground and enraging the Lava Men. They attack, but Thor keeps them at bay and demands to see their kind. Then they melt the ground beneath Thor's feet, but he is protected from the lava by the power of his hammer, and he soon confronts the witch doctor and the king. When they tell him how the Living Stone came into their possession and of their plot to conquer Earth, he realizes that striking it with his hammer could destroy the world.
The witch doctor then orders an attack, and Captain America battles a squad of Lava Men until they enclose him in hardened cinder. As Iron Man staves the subterranean creatures off, Giant Man and the Wasp, reduced to ant size, investigate the rock and discover an area where it can be struck without causing a cataclysm. They go in search of Thor, but when they find the embattled Iron Man, Giant Man uses the team's helicopter to blow the Lave Men back to their domain. Iron Man then frees Captain America from the cinder cocoon, and they all meet Thor under ground.
Bruce Banner unexpectedly changes into the Hulk and starts battling the Avengers, and the witch doctor, observing from a hidden vantage point, fortuitously changes Thor into Donald Blake with his radioactive rod, thus preventing him from destroying the rock. Fortunately, the remaining Avengers trick the Hulk into striking the rock at proper spot and the object implodes, ending the crisis. Blake soon recovers, becomes Thor, and warns the Lave Men never to threaten the surface people again. As Banner, who was changed back from the Hulk by the implosion, leaves quietly with Betty. The Avengers regroup just in time to receive an emergency radio message from Teen Brigade.