Cannibal Holocaust is well known as an exploitation film because of controversies following its release. After premiering in Italy, the film was seized by a local magistrate, and Deodato was arrested on obscenity charges. He was later accused of making a snuff film because rumors claimed some actors were killed on camera. Although Deodato was later cleared, the film was banned in Italy, the UK, Australia, and several other countries due to graphic gore, sexual violence, and because six animals were killed on camera.
There are two timelines in the film, one depicting Monroe's trip into the jungle to determine the fate of the American explorers, and the other involving Monroe's subsequent viewing of the recovered films made by the missing explorers. Much of the film is the depiction of the recovered film's content, which functions similarly to a flashback and grows increasingly disturbing as the film progresses.
The film begins with a television documentary about a missing film crew and its expedition into the Amazon Rainforest to make a documentary about cannibal tribes. The crew consists of Alan Yates, the director; Faye Daniels, his girlfriend and script girl; and their two friends and cameramen, Jack Anders and Mark Tomaso. Professor Harold Monroe, a New York University anthropologist, volunteers to lead a rescue mission to find the team. He flies to the Amazon and meets Chaco and Miguel, two guides who will assist him in his mission. Due to a local military raid, the group has a hostage from a tribe called the Yacumo to help them negotiate with the natives. After a long trek through the jungle, they happen upon a Yacumo male raping and murdering his wife as a punishment for adultery. The group follows the lone Yacumo to a large clearing, where Miguel negotiates the release of their hostage if the Yacumo let them in their village.
Upon arriving to the village, the rescue team is greeted with hostility. It is soon revealed that the last white men to visit the tribe, the missing film team, caused great unrest. Miguel quells the tribe's fears by giving the chief a switchblade as a sign of good faith. The next day, the Yacumo leads the group to the edge of their territory, where two vicious cannibal tribes, the Yanomamo and Shamatari, are perpetually at war with each other. Monroe’s team follows a group of Shamatari warriors to a riverbank, where they save a smaller group of Yanomamo from certain death. As a token of gratitude, the group is invited to the Yanomamo village but, once there, they are again treated with hostility. In an attempt to gain their trust, Monroe bathes naked in a river, which a small group of Yanomamo women find amusing. They lead Monroe to a shrine made out of the bones of the lost film team, confirming Monroe’s worst fears. Frustrated, Monroe confronts the tribe in their village and plays a tape recorder for them, which he is able to exchange for the footage that the missing film team shot.
Once Monroe is back in New York, the executives of the Pan American Broadcast Company inform him that they want Monroe to host their airing of the film team’s documentary. Monroe asserts that he will only do it if he views the film reels first. The executives agree and to introduce Monroe to the works of Alan Yates, they show him a short segment from one of the team's previous documentaries, The Last Road to Hell. After viewing, a female executive tells him that the documentary was staged by Yates to acquire more exciting footage. Puzzled, Monroe continues on to view the footage recovered from the Amazon.
The first film reel begins with the group embarking on their trek deep into the jungle, eventually making camp and slaughtering a turtle for food. The next day the group’s guide, Felipe, is bitten in the foot by a poisonous snake and, despite Jack cutting off his leg, Felipe dies. After burying him, the film team continues on to locate the Yacumo. They come across a small group of Yacumo in a clearing, where Jack shoots one in the leg so the group can follow him to the village at their leisure. As the projectionist changes reels, Monroe comments on his disapproval of the team's actions, stating they should have found other ways to introduce themselves to the tribe. The second reel then starts, showing the group’s arrival at the village, where they almost immediately round up the entire tribe into a large hut and burn it down in order to stage a scene for their documentary, in which the Yacumo were slaughtered by the Yanomamo. Monroe again expresses his concerns about the staged scenes and the unethical treatment of the natives, but his worries are ignored. He continues to view the reels the next day, in which the group films a pregnant Yacumo woman having her fetus forcibly removed.
At the station, Monroe expresses his disgust toward the executives' decision to still air the documentary. To change their minds, he volunteers to show them the unedited footage. The final two reels begin with the film team locating a young Yanomamo girl, whom the men gang rape as Faye tries to stop them. The projectionist changes to the final reel, which begins with the group arriving at the site where the same girl is impaled on a pole, claiming the natives killed her because of an “obscure sexual rite.” After the group moves on, the Yanomamo attack them in revenge for the girl’s death. Jack is impaled by a spear, but instead of attempting rescue, Alan shoots him so he and Mark can film the natives emasculating, dismembering, cooking, and eating his corpse. Afterwards, while the remaining three attempt escape, Faye is captured by the Yanomamo, and Alan insists that he and Mark try to save her. Mark films as Faye is gang-raped and beheaded, after which the cannibals locate the final two in their hiding spot. The camera drops to the ground, and Alan’s bloody, blank face falls in front of the lens as the reel ends. At first silent, the executives order the footage to be burned as Monroe leaves the station.
