The film picks up right after the dramatic conclusion of King Kong, set a decade later as the legendary ape is kept alive at Atlanta University. Under the stewardship of Amy Franklin, the team of doctors strives to keep King Kong alive, relying on an artificial heart that is desperately needed due to his failing original organ. However, the procedure hinges on securing enough plasma, a challenge that requires a miracle.
Meanwhile, in the heart of Borneo, adventurer Hank Mitchell stumbles upon another colossal ape, this time a female who quickly takes a liking to him. In a precarious situation, the locals fire tranquilizer darts at her, allowing Mitchell to capture the creature. News of this incredible find reaches the university, which persuades him to hand over the female ape for plasma use in Kong’s surgery, as well as to study her further.
After her transport to the U.S., Lady Kong finds herself confined in a warehouse while her new habitat is being constructed. Yet, she has a peculiar sense that King Kong is close by. Soon, the doctors successfully replace King Kong's heart, and upon awakening, he instinctively senses Lady Kong's presence. Mitchell urges the university to expedite Lady Kong's transfer, sensing impending chaos.
As they attempt to move Lady Kong, her distress triggers King Kong's fury, prompting him to break free from confinement. He devastates the area to rescue her, and the two escape into the dense wilderness together. Meanwhile, the U.S. Army, led by Lt. Col. R.T. Nevitt, is determined to recapture the giant apes, obstructing access to them and complicating [Franklin]'s and Mitchell's efforts.
Despite their best attempts, King Kong disappears the next morning, leaving Lady Kong alone. In a desperate bid, the Army uses helicopters to sedate Lady Kong. When King Kong charges in to protect her, military forces bomb the area to keep him at bay. They successfully capture Lady Kong, while King Kong, desperate but cornered, makes an incredible leap to escape but suffers a devastating head injury that leaves him presumed dead.
Three months pass as Lady Kong is confined in an abandoned missile silo, away from public sight. Franklin manages to secure a brief visit, sensing the ape's sorrow as she refuses to eat, pining for King Kong. Mitchell returns from Borneo with a proposal to acquire land for the Kongs but learns of Lady Kong's dire situation. Frustrated, he tries to seek answers but is shooed away.
Meanwhile, King Kong has managed to survive in the swamps, his resilience keeping him alive by consuming local alligators. He suddenly becomes aware of Lady Kong's distress calls and sets off to rescue her. As his path intersects with a nearby village, his presence causes panic, alerting Col. Nevitt's team to his whereabouts.
Four hunters ambush King Kong with dynamite, but their plan backfires. Captured and tortured, Kong responds with fury, ultimately killing the hunters. Realizing he needs to save Lady Kong, he sets out for the silo, not deterred by the looming threats from the Army.
In a climactic showdown, King Kong confronts the military defenses just as Franklin and Mitchell prepare to free Lady Kong, only to discover she is pregnant. The rescue unfolds, but chaos ensues as she goes into labor, collapsing in a barn during the Army's relentless attack. Enraged and wounded, King Kong takes down the forces targeting him, culminating in the death of Col. Nevitt.
In a heart-wrenching finale, King Kong witnesses the birth of his son before succumbing to his injuries. Ultimately, Lady Kong and her offspring are returned to Borneo, carrying on Kong's legacy as the cinematic saga of the great apes comes to a poignant end.
