On the Amazon River, a desperate poacher named Danny Trejo finds himself in a perilous situation as he hides in his boat from an unseen creature. In a tragic attempt to evade death, he takes his own life by shooting himself just as the creature breaks through his vessel.
At the same time, a dedicated film crew is busy documenting the elusive Shirishamas, a long-lost indigenous tribe of the Amazon. This crew comprises director Terri Flores, her childhood friend and cameraman Danny Rich (Ice Cube), production manager Denise Kalberg (Kari Wuhrer), her boyfriend and sound engineer Gary Dixon (Owen Wilson), narrator Warren Westridge (Jonathan Hyde), and anthropologist Professor Steven Cale, alongside boat skipper Mateo (Vincent Castellanos).
Their journey takes a turn when they meet snake hunter Paul Serone, who persuades them to allow him to guide them deeper into the Amazon in pursuit of the Shirishamas. This venture stirs romantic tension between Danny and Terri as they navigate their ship down the river. Serone reveals that the tribe worships anacondas, claiming these immense snakes are revered as both gods and guardians.
Tensions rise as the crew becomes increasingly uneasy around Serone, and Cale finds himself frequently clashing with him over the authenticity of Serone’s claims about Shirishama culture. A crisis occurs when Cale suffers an allergic reaction, leaving him unconscious. Though Serone performs an emergency cricothyrotomy to save him, he soon seizes control of the boat, insisting they continue their journey deeper rather than retreat for medical assistance. A disastrous detour, initiated by Serone blowing up a barrier, results in the loss of their escape boat and serves only to further entrap the crew in Serone’s wild plans to capture a legendary giant anaconda.
The situation escalates when Mateo falls into the water, becoming the first victim of the lurking monster. The crew, in disarray, tries to locate him while Serone uses the chaos to his advantage, killing a monkey as bait for the anaconda, much to Terri's dismay. In a bid for survival, Serone asserts his authority by wielding the only guns available. As the night progresses, the horrifying presence of the anaconda makes itself known, leading to a tragic confrontation where Gary is crushed by the snake, and Serone incapacitated Terri when she attempts to save him.
Determined and desperate, the crew retaliates against Serone and ties him up as punishment. They soon find themselves challenged yet again when their boat becomes stuck at a waterfall. As chaos reigns in the water, Serone’s true merciless nature emerges as he decisively eliminates Denise to ensure his survival.
Yet the anaconda remains an omnipresent danger, as Westridge bravely distracts it, allowing Terri and Danny to escape but ultimately sacrificing himself in the process. In the ensuing battle against the beast, Cale wakes just in time to help, but as Danny wrestles with Serone, he’s ultimately thrown into the river.
In a final desperate act, Serone attempts to use Terri and Danny as bait for an even larger anaconda, but in a twist of fate, it becomes his nemesis, swallowing him whole. Terri, finding refuge in an abandoned structure, discovers a nest of newborn anacondas, leading to a heart-pounding chase. Danny, showcasing unexpected heroism, manages to pin the anaconda’s tail and ignite a fire that propels the creature into the water in a fiery explosion.
As the dust settles, Danny and Terri regroup with the recovering Cale. While drifting downriver, the trio is unexpectedly met by the Shirishama tribe, who graciously assist them in their escape from the grips of the Amazon.
