A SEAL commander calls in Pete Thornton and MacGyver to watch a training drill, and then explains that the Navy needs their help. A group of modern-day pirates are using SEAL techniques to attack and rob boats on the high seas, giving the organization a black eye. The Navy can't get involved in a civilian matter so they want the Foundation to help.
Gar Manning and his partners Matt Bell and Jack Rogan are operating from a cigarette boat. They watch as Dr. Barbara Ortega and her assistant Paul Engle bring up a chest from a sunken ship on the ocean's floor. Manning and Bell swim across in SCUBA gear while Ortega opens the chest. Inside is a small amount of Spanish treasure and the ship's document boat. Inside is the log, which Ortega determines lists the course corrections they need to locate the main fleet.
Manning and Bell send up a distress balloon indicating a diver in distress. When Ortega and her crew try to pull up the diver, the pirates board on the other side of their ship and take them at gunpoint. They lock Ortega and her people below and Rogan brings over the boat. They load the treasure onto it, fire a few rounds to force Ortega to stay below, and then drive away before she can get a glimpse of their boat.
Later, MacGyver learns of the third robbery and goes to see Ortega at her research center and museum. Meanwhile, Manning and his men go to a boatyard to trade their cigarette boat in for a ketch. As the yard's owner, Arne Lindquist, looks over the cigarette boat, Manning explains to the other two that it's time to dump their original boat and buy something they can quietly sail away with after they sell the loot. To sell the treasure, Manning figures his best bet is to talk to Ortega.
Ortega shows MacGyver around her museum of undersea finds and talks about how the center needs the money they would have gotten from the salvage. Manning, disguised as a tourist, approaches her as they look at some treasure and casually asks where one could sell such pieces. After she answers him and he leaves, Ortega talks about how her father's dream was to find the $60 million in missing treasure and return it to the rightful owners, the Spanish-American people. When her father died in an accident, Ortega vowed to carry on his dream. As they discuss the $60 million and the ship's log, they're unaware that Manning is listening in.
Next, MacGyver takes Ortega to the Phoenix Foundation. He and Pete play back recordings of ship engines and she identifies the one that matches the pirates' boat.
The pirates hole up in a hotel room packing away the treasure. Manning explains that they can abduct Ortega and force her to translate the ship's log and lead them to the treasure. The next day, Rogan and Bell follow her to the docks where she's conducting tours for Spanish-American children injured in wars. MacGyver arrives and one of the kids, Christobel, wonders if he's Ortega's boyfriend. Rogan listens in as Ortega says that she put out a reward for information on the cigarette boat and Arne Lindquist contacted her. The pirates go to see Lindquist and Manning kills him. They pick up the ketch and wait for Ortega to arrive.
That night, Rogan impersonates Lindquist and sets up a meeting with Ortega at the boatyard. She and MacGyver go there and realize they've been tricked when the pirates capture them. MacGyver blinds them temporarily by blowing packing pellets at them. He runs outside and draws their attention, while Ortega tries to escape in the van. Manning captures her, while Rogan and Bell corner MacGyver on an old boat. He tosses a gas can overboard to make them think he's dove underwater, but accidentally knocks over a can. Manning has them lock the hatch and then shoots the boat with holes, causing it to sink.
As the pirates leave in their ketch, MacGyver tries to find a way out of the rapidly sinking boat. He finally wedges a board beneath the hatch's latch, inserts a buoy, and tries to inflate it with water using the bilge pump. When the bumper cracks from the stress, MacGyver knocks the valve off of a canister of compressed gas and shoots it upward through the hatch, making his escape.
The next morning, they call in the SEAL commander and try to locate the ketch. The file on Manning shows that the SEALs rejected him so he decided to get revenge by using their own techniques for piracy. The only possible hiding place is an old island that's used as a dumping ground for naval ordinance. They figure that a risktaker like Manning would use it despite the potentially live rounds on the island.
Pete and a Foundation pilot take a fishing boat out near the island, make a wide turn, and dump out MacGyver, who's wearing SCUBA gear. He swims to shore, removes his gear, and proceeds inland. Meanwhile, Manning and his men have holed up in an old artillery bunker. He has Ortega working on the ship's log and boasts that no one will ever look for them there.
MacGyver narrowly avoids one undetonated missile but hits a tripwire to an anti-personnel mine that Manning placed. Using a piece of string, MacGyver holds the tripwire taut until he can get clear. He jumps clear of the resulting explosion, only to land on another land mine. He jams the trigger button with a twig but discovers that it's dud. Pocketing it, he continues toward the bunker. Meanwhile, Manning hears the mine explodes and sends Rogan and Bell to investigate.
The two pirates split up and the nervous Rogan stumbles across a tripwire. MacGyver pokes him in the back with a stick to convince the pirate he has a gun, and then ties him up.
Manning is getting increasingly nervous and Ortega mocks him, warning that she's just about finished but it won't do him any good. Manning boasts that Bell is an expert with an Uzi and will take out any intruders.
Bell spots Rogan, propped up on some brush and seemingly dead with a wooden shaft through his chest. When Bell approaches his comrade, he discovers that Rogan is alive. MacGyver, hiding in the brush, punches Bell unconscious and then ties the two men together.
At the bunker, Manning finally breaks and takes Ortega outside to use her as a hostage. MacGyver is waiting atop the bunker. He threatens to toss the landmine and blow them up, and Ortega tells him to do it. MacGyver tosses the dud landmine to Manning, who drops his gun to catch it. MacGyver jumps on him and the two men struggle, and MacGyver tells Manning not drop the mine. Manning freezes and MacGyver knocks him out.
Later, MacGyver is at the Phoenix Foundation practicing soccer with Christobel. He tells Ortega that the Foundation is donating a king-sized dive boat to help search the treasure. When Ortega wonders where they're going to find enough divers, MacGyver assures her that the grateful SEAL divers are volunteering their efforts to recover the treasure for the children.