The film follows former dolphin trainer and activist Ric O’Barry’s quest to document the dolphin hunting operations in Taiji, Wakayama, Japan. In the 1960s, O’Barry helped capture and train the five wild dolphins who shared the role of “Flipper” in the hit television series of the same name. The show, very popular, fueled widespread public adoration of dolphins, influencing the development of marine parks that included dolphins in their attractions. After one of the dolphins, in O’Barry’s opinion, committed a form of suicide in his arms by closing her blowhole voluntarily in order to suffocate, O’Barry came to see the dolphin’s captivity and the dolphin capture industry as a curse, not a blessing. Days later, he was arrested off the island of Bimini, attempting to cut a hole in the sea pen in order to set free a captured dolphin. Since then, according to the film, O’Barry has dedicated himself full-time as an advocate on behalf of dolphins around the world.
After meeting with O’Barry, Psihoyos and his crew travel to Taiji, Japan, a town that appears to be devoted to dolphins and whales. In a nearby, isolated cove, however, surrounded by wire fences and “Keep Out” signs, an activity takes place that the townspeople attempt to hide from the public. In the cove, a group of Taiji fishermen engage in dolphin drive hunting. The film states that the dolphin hunt is, in large part, motivated by the tremendous revenue generated for the town by selling some of the captured dolphins, female bottlenose dolphins, to aquariums and marine parks and killing the majority of the rest. The dolphins that are not sold into captivity are then slaughtered in the cove and the meat is sold in supermarkets. According to the evidence presented in the film, the local Japanese government officials are involved in the hiding of the hunting, and the Japanese public is not fully aware of the hunt and the marketing of dolphin meat. The film states that the dolphin meat contains dangerously high levels of mercury and interviews two local politicians, Taiji City Councilmen, who have, for that reason, advocated the removal of dolphin meat from local school lunches.
Attempts to view or film the dolphin killing in the cove are physically blocked by local police and the Japanese local government who treat the visitors with open intimidation, derision, and anger. Foreigners who come to Taiji, including The Cove’s film crew, are shadowed and questioned by local police. In response, together with the Oceanic Preservation Society, Psihoyos, O’Barry, and the crew utilize special tactics and technology to covertly film what is taking place in the cove. The film also reports on Japan’s alleged “buying” of votes of poor nations in the International Whaling Commission. The film indicates that while Dominica has withdrawn from the IWC, Japan has recruited the following nations to its whaling agenda: Cambodia, Ecuador, Eritrea, Guinea-Bissau, Kiribati, Laos, and the Republic of the Marshall Islands. This is not entirely accurate, however, as Ecuador has been a strong opponent of whaling. At the end of the film, O’Barry shows footage of the Taiji dolphin slaughter to a Japanese official, after the official repeatedly denies the incident; he is unmoved by the footage, and asks O’Barry where he obtained it. The film then cuts to a scene showing an annual meeting of the International Whaling Commission. O’Barry marches into a meeting of the Commission strapping a TV showing the footage on his chest (while the Japanese delegates are talking about how they have improved Whaling tactics). O’Barry walks around the crowded meeting room displaying the images until he is escorted from the room.