Pete brings in MacGyver to tell him that Billy Colton has stolen a confidential file on the Foundation's endangered species program. A major poacher, Ladysmith, who traffics in rhino horn is still at large despite the Foundation hiring Billy's brothers to find him. In Billy's locker they found a map with the word Nabo circled on a map of Kambezi. Kate Hubley runs the local nature preserve, the Nabo Ranch. Pete figures Billy decides to prove something to his brothers, accessed the file, headed to Kambezi, and plans to collect the reward. He also charged his ticket to the Foundation.
MacGyver goes to Africa and visits the Nabo Ranch. When he arrives, Kate is conducting a funeral for Sam, a ranger who was killed by poachers while guarding the ranch's stockpile of rhino horns. Kate plans to burn the horns, worth millions of dollars on the black market, as a message to the governments of the world to enforce the import ban on rhino horns. General Mabuto and his lieutenant, Zimba, are also in attendance. After introducing himself to Kate, MacGyver talks to Mabuto, who regrets that he doesn't have enough manpower to protect Nabo Ranch. After he leaves, MacGyver shows Kate a photo of Billy, but she's never seen him.
Billy is undercover as a worker at the Nabo Sugar House, a refinery. Ladysmith arrives and meets with his secret supplier: General Mabuto. Billy listens in as Ladysmith informs Mabuto that he is going to a resort later to meet with Chan, the only buyer capable of buying their entire shipment. Ladysmith, a racist, quickly gets on Mabuto's nerves and the general draws a knife on him while warning him if he doesn't get the money, he's a dead man.
Kate gets word that poachers are in the area. She and MacGyver drive to the scene where two of her rangers have captured a poacher. Unfortunately, the poacher already used a chainsaw to cut off the horn from a still-living black rhino. Kate has no choice but to shoot the rhino and put it out of its misery.
They question the poacher, who mentions the Nabo Sugar House. Kate realizes Billy must have gone there and insists on going with MacGyver to check it out. Meanwhile, Billy checks the boxes on the board that Mabuto is using to ship the rhino horns. Zimba spots Billy and captures him. Billy tries to fake being a local tribesman but Mabuto realizes he speaks English. He then claims he's Ladysmith's man, working undercover to guard the shipment. Mabuto is happy to execute him as message to Ladysmith. MacGyver sneaks in just in time to witness two of Mabuto's men preparing to hang Billy. He has Kate drive a Jeep while he uses a machete to cut the rope, then get Billy into the Jeep so they can make their escape.
Back at Nabo Ranch, Billy gets into an argument about MacGyver over his trying to catch Ladysmith on his own. Billy explains that he tracked down Ladysmith by investigating escrow houses to see what properties the poacher owns. Once he checked out the Sugar House, he learned that Ladysmith is also apparently smuggling out drugs hidden in the sugar packets. MacGyver filters the sugar and discovers that the packets contain powdered rhino horn. Ladysmith is selling to both sides of the market, both for powdered rhino horn and the intact horns. Billy tells them about Ladysmith's meeting with Chan and MacGyver figures he'll take Chan's place. However, he's going to need Billy's help.
The trio goes to the resort and learns which room Chan is in. Billy dresses as a waiter and makes a delivery to Chan's room, then knocks him out. Meanwhile, MacGyver approaches Ladysmith and claims to be Chan's partner. He wants to see the horns before they make the payoff. Ladysmith refuses and starts to leave, but Kate comes over and convinces him that's how Chan does business. Ladysmith agrees and sets up the exchange at a nearby hydroelectric dam. However, he insists that Kate go with him and that they don't get the rhino horns until he sees the money. MacGyver isn't thrilled with Kate interfering, but she insists she knows what she's doing and gives him directions to get there first.
MacGyver and Billy get to the dam first and spot the boat. They also spot Mabuto and Zimba on the bridge, and MacGyver realizes that if Mabuto sees Kate, it will ruin everything. They quickly get down to the dam riding a water flume and then climb up to the bridge.
Ladysmith and Kate arrive and she stays in the car while the poacher meets with Mabuto. Kate sees Mabuto and attempts to conceal her face with the sun visor. Mabuto realizes something is wrong and comes over, then recognizes Kate. MacGyver crawls under the car and gets in, then slams the car door into Mabuto and Zimba as they prepare to shoot Kate. Billy trips Ladysmith when he draws a gun, and the poacher runs away. MacGyver goes after him, and the two struggle on the edge of the bridge. They both fall over, and Ladysmith clings to MacGyver's legs. He loses his grip and falls to his death onto the boat below, landing on the rhino horns.
Later, Kate holds the horn burning ceremony in front of representatives of world governments. She thanks MacGyver and Billy for their help. Billy announces that he plans to take on another case his brothers failed to solve, using the reward to finance his trip. MacGyver suggests he donate the reward money to Nabo Ranch instead and Billy agrees. Kate sets the horns on fire and asks the government representatives to enforce the import ban. MacGyver wonders if it will do any good.