A ramshackle motor boat, named Maria, slowly chugs its way along the Ambro River, in the jungles of South America. Aboard is a businessman called Blackmer; his destination is a remote house belonging to the reclusive scientist Dr. Orchard, who greets his visitor as Maria arrives at his dock. From the local plant Sidonicus americanus, Orchard tells his visitor, he has developed a food additive called "Theramine" which, if fed to animals, causes them to grow - considerably beyond their natural size. Such enlargement of animal stock around the world, he believes, would offer a simple solution to famine, along with other financial advantages. Unknown to either of them, however, someone else is furtively eavesdropping on their conversation...
That "someone" is Blackmer's boatman, Culp. When a storm forces Orchard's two visitors to stay at the river house for the night, Culp resolves to abscond with the Theramine and use it to become rich. He waits until the other occupants are asleep...then quietly lifts the keys to Orchard's laboratory from the housekeeper, Mrs. Files, and steals down to the basement laboratory. While filling a vial with a quantity of Theramine, Culp accidentally knocks the rest into a sink, and the chemical drains into the river...
The next morning, Blackmer and Culp board Maria and depart Orchard's house. But their journey downriver ends in disaster, when Maria is smashed into kindling by an enraged alligator - one now expanded to an extraordinary size! Orchard's assistant, Hector McGill, manages to rescue Blackmer, but Culp has vanished, and is presumed dead. Three giant alligators quickly surround the river house and proceed to attack it - with Orchard, McGill, Blackmer and Mrs. Files now trapped inside.
Oversized alligators attacking the house where Blackmer, Mrs. Files, Dr Orchard, and his assistant, Hector McGill, are trapped.
On Mrs. Files' advice, McGill contacts International Rescue. Up on Thunderbird 5, John is incredulous - "Giant alligators!?" - even as he relays the incredible details to Tracy Island. Jeff orders the launch of Thunderbird 1 and Thunderbird 2 (carrying Pod 4)...
Arriving at the danger zone, Scott takes to his hoverjet and uses its missiles to ward off the alligators from the area around the river house, long enough to allow him to enter through the laboratory window. By now, the alligators have caused so much damage that the laboratory eventually caves in, forcing Scott and the others to escape to the lounge...where they're confronted by none other than a very-much-alive Culp, who shoots Scott's gun from his hand and proceeds to hold them all at gunpoint...
Virgil arrives in Thunderbird 2, and uses its vertical thrusters to repel the alligators away from the house. Alan and Gordon, manning tranquilliser guns, subdue two of them. When the third alligator returns to the river house - and against his brothers' orders - Alan leaves TB2 on his own hoverjet, attempting to lure it away, successfully at first. But then, failing to see a tree in his path, Alan falls and then slumps unconscious. Gordon saves his brother, by neutralising the 'gator. Meanwhile, Culp is threatening to pour the entire vial of Theramine into the river, if he is not granted safe passage upstream. Gordon launches Thunderbird 4 into the river, and discovers a fourth, even larger, alligator - which attacks Culp's escape-boat and kills him before being itself killed by Virgil, with a missile from TB2. Gordon then suits up in diving gear and takes to the river, searching for the now-missing vial of Theramine. Despite fears that it may been smashed, Gordon retrieves it, intact...
Back on Tracy Island, Jeff announces that Orchard and Blackmer are putting international restrictions on Theramine. And Tin-Tin, who's been away from the island on a shopping trip, tells Alan that she has purchased a special present for his upcoming birthday. It is revealed to be...a pygmy alligator!