The movie follows former dolphin trainer 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, a pop-culture phenomenon, 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 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 the small town of Taiji, a town that appears to be devoted to the wonder of the dolphins and whales that swim off the town's coast. 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 a large part, motivated by the tremendous revenue generated for the town by selling some of the captured dolphins to aquariums and marine parks. The dolphins that are not sold into captivity are then slaughtered in the cove by the fishermen and the meat is sold in supermarkets. According to anecdotal evidence presented in the film, most Japanese throughout Japan are unaware of the hunt or the marketing of dolphin meat. The film states that the dolphin meat contains dangerously high levels of mercury and profiles local Japanese politicians who have, for that reason, advocated the removal of dolphin meat from local school lunches.
Attempts to view or film the dolphin culling in the cove are physically blocked by local volunteers 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 the 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 the alleged "buying" by Japan of votes 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 the nation of Ecuador has been a strong opponent of whaling. At the end of the film, O'Barry marches into a meeting of the Commission carrying a TV showing footage of the Taiji dolphin slaughter. O'Barry walks around the crowded meeting room displaying the images until he is escorted from the room.