Dr. Starbuck rescues Aquaman from an underwater landslide and then declares war on the surface world. In Aquaman’s absence, Aquababy is king of Atlantis.
Responding to a distress call from Captain "Forty Knot" Bradley, Aquaman and Aqualad are asked to clear an obstruction preventing the ship from retracting it's anchor. The obstruction turns out to be a sperm whale battling against a giant squid. The two sea creatures have become entangled in the anchor chain, in the midst of their blood feud. Their killing frenzy is so great that they ignore Aquaman's telepathic commands to cease fighting. Aquaman and Aqualad push the ship's anchor into a nearby volcanic "blow hole". The intense heat of the burning magma travels through the anchor, up the chain, to the warring marine creatures. When the chain becomes too hot to bear, the sea creatures end their struggle, and move away from the anchor chain, and each other. Freed of encumbrance, the anchor begins to slowly ascend to the surface. En route back to Atlantis, Aquaman and Aqualad are caught in an undersea explosion, and buried under a veritable mountain of coral. They are rescued by Dr. Starbuck, and his amazing animal companions, Boduhr, a gorilla, and Krakka, a sea eagle. Dr. Starbuck, a marine biologist, has perfected a method of turning air breathers into water breathers. Having abandoned life on the surface, Dr. Starbuck asks Aquaman for refuge in Atlantis. Aquaman goes one better, and, after showing Dr. Starbuck around the great domed city, proclaims him an honorary Atlantean and chief advisor to the throne. Just then, Topo arrives with another distress call from the surface. Aquaman and Aqualad mount up on their respective sea steeds, Storm and Imp. Bidding their farewells to Mera and Dr. Starbuck, the two heroes ride out of the city. Crossing over the Dungeon Depths, Aquaman and Aqualad are struck by giant bolos. Knocked from their sea horses, they plummet into the Dungeon Depths.
When Storm and Imp return to Atlantis riderless, Mera fears the worst. Placing her infant son on the throne, she bestows regent status on Dr. Starbuck, giving him the power to rule over Atlantis in her son's name. Mera then departs to search for Aquaman and Aqualad. Mera, however, never makes it out of the city. Dr. Starbuck drugs her and locks her away in a palace basement. Several days later, Boduhr and Krakka, leading a contingent of Atlantean soldiers, attack and destroy a desalinization plant on the surface. Captain Bradley, alerted to the attack, arrives at the scene, and orders his fleet to begin releasing depth charges on the Atlantean invaders. Bradley, however, is too late. The Atlanteans are already long gone. When questioned about this new course Dr. Starbuck has set for Atlantis, the deranged scientist states that the desalinization plant was removing vital minerals and nutrients from the water, that the Atlanteans need for their farms. It had to be destroyed. The Atlanteans seem placated by Dr. Starbuck's reasoning, and thus, a few days later, the Atlanteans join Boduhr and Krakka, in attacking a surfacing nuclear submarine. The submarine rapidly dives to escape the assault, then radios Captain Bradley regarding the incident. With Aquaman refusing to answer his distress signals, Captain Bradley sees no choice but to order the fleet to seek out Atlantis... and destroy it. The Atlanteans continue to voice concern over Dr. Starbuck's "well-meaning" efforts to preserve the safety and security of the underwater city. Nonetheless they continue to comply with his commands to assault surface targets. Unable to discern the location of Atlantis, Captain Bradley orders the fleet to begin dragging the seas with grappling hooks, set at the greatest depths. One such hook descends all the way down into the Dungeon Depths. Aquaman and Aqualad escape the strange heavy water, that has kept them from ascending to freedom, by clambering up the grapple hook's chain.
Returning home, Aquaman and Aqualad are stunned to see Atlanteans dragging Navy frogmen, in chains, through the streets of Atlantis. Aquaman stealthily frees one of the frogmen, and then takes his place in the procession. Aqualad returns the man to the surface. Placed in a cage with the other Navy divers, Aquaman learns of the Atlantean war against the surface, propagated by Dr. Starbuck, in Arthur, Jr.'s name. The Navy divers are quick to recognize Aquaman in their midst. They inform him that they are equipped with a radio homing device, that, even now, is leading Captain Bradley's fleet to Atlantis. Aquaman is released from the cage, and brought before his son, the "King", and Dr. Starbuck, the King's regent. Dr. Starbuck interprets Arthur, Jr.'s infantile gibberish as a request for a fight to the death between the "Navy diver" and Boduhr, Dr. Starbuck's aquatic gorilla. Like a Roman gladiator, Boduhr is armed with a net and trident. A fierce combat ensues. Aquaman strikes the ape, again and again, to no avail. Boduhr is able to entangle Aquaman in the net, and bring him forcefully down onto the sea floor. The impact knocks the scuba gear loose, revealing Aquaman's face to the Atlantean court. Dr. Starbuck declares Aquaman a traitor, and in league with Atlantis' enemies on the surface. "Speaking" for Arthur, Jr., Dr. Starbuck demands Boduhr deliver the killing blow. Boduhr thrusts his trident down on Aquaman, but it is deflected by a hard water sphere, projected by Arthur, Jr. Aquaman then uses the self same sphere to bludgeon Buduhr senseless. The Atlanteans rise up against Dr. Starbuck. Krakka swoops in to attack Aquaman. The Sea King uses Boduhr's net to ensnare the aquatic sea eagle. Meanwhile, on the surface of the sea, Aqualad, returning the navy diver that Aquaman had rescued and impersonated, bears witness to Captain Bradley ordering the fleet to release depth charges on Atlantis. Aqualad dives down to warn Atlantis of it's impending doom, only to find the entire city protected underneath a hard water shield, created by Queen Mera. The city saved from destruction, Aquaman turns Dr. Starbuck, and his amazing aquatic animals, over to Captain Bradley.