The film opens with Charles Travis, played by Bruce Campbell, an employee at TraviCom, who is testing a diamond-powered communications laser in a secluded region of the Congo, specifically near a dormant volcano. Charles's excitement is dampened when his friend Jeffrey meets a gruesome fate after entering a cave, leaving Charles horrified as an unseen creature attacks him. Back in Houston, Dr. Karen Ross, portrayed by Laura Linney, anxiously awaits communication from Charles. She and her team are stunned when they receive a video feed showing a scene of destruction and death at the camp, abruptly cut short by a swift attack from a shadowy creature.
R.B. Travis, the CEO of TraviCom and portrayed by Baker, reveals that the aim of this venture is to discover a rare blue diamond believed to be located at volcanic sites, hoping to enhance their communication technology. He sends Karen, a former CIA operative, to find Charles and complete the mission, promising her that his intention is to locate his son rather than simply gather riches.
Meanwhile, Dr. Peter Elliott, a young primatologist played by Dylan Walsh, partners with his assistant Richard to teach human communication to their gorilla, Amy, voiced by Shayna Fox. They have created a method to translate her sign language into a digitized voice, but Peter grows increasingly concerned about Amy's psychological state, especially after she begins painting recurring images of an eye surrounded by trees. Upon realizing she has been dreaming of a jungle, he plans to return her to Africa, but the university is reluctant to fund the undertaking. Herkermer Homolka, brought to life by Tim Curry, approaches Peter with financial backing for the expedition. Karen joins Peter on this journey, eager to search for Charles.
Upon their arrival in Africa, they encounter Captain Munro Kelly, an expert guide who briefs them about Homolka's previous failed expeditions in search of the legendary "Lost City of Zinj." The team crosses the Zaire border covertly but must parachute into the jungle when their aircraft is unexpectedly shot down. While establishing camp, Karen sets up equipment to reach out to TraviCom, but chaos ensues when playful antics between Peter and Amy disrupt the connection. Misunderstanding this mishap as another attack, Travis hastily dispatches reinforcements.
The following day, members of a ghost tribe lead the team to an apparent casualty from the previous expedition, Bob, who is alive but catatonic. As they attempt to revive him, he reacts to Amy in sheer terror, dying from shock. Confusion and fear set in as the team delves deeper into the jungle, even facing a harrowing hippopotamus encounter. Through the tale spun by Homolka, it becomes clear that Amy's haunting artwork might just hold the key to locating Zinj.
The group eventually discovers Zinj, even as the volcano begins to awaken ominously. As they carefully explore the ruins, they find themselves besieged by a series of horrifying events, including the sudden death of Richard, who is attacked by a sinister gray gorilla. Turmoil escalates at night when gray gorillas assault their camp, only to be fended off by Karen's automated defenses. In the aftermath of this chaos, Homolka deciphers the repeating hieroglyphics: "We are watching you."
The team revisits the ruins of Zinj to uncover Homolka and the fabled diamond mine. While greed overtakes him, leading to his demise at the hands of the gray gorillas, Karen and Peter discover Charles's lifeless body cradling a precious blue diamond. Tragedy strikes as they are outnumbered and attacked, forcing Amy to bravely defend Peter against the relentless gorillas. Seizing the moment, Karen utilizes one of the diamonds, channeling its energy through her laser as they escape the tumult of the volcano's eruption.
In the aftermath of their escape, Karen contacts Travis, sharing her heartbreaking discovery. However, realizing that Travis only cares for the diamonds, she takes definitive action. She sets her laser to obliterate TraviCom's satellite, severing ties with the corporation. As the survivors salvage a hot air balloon from the remnants of their expedition, Peter bids farewell to Amy, who steps back into the wild. The group ascends into the twilight, leaving behind both treasures and tragedies, while Amy watches on, a symbol of the profound bond forged in their harrowing journey.
