MacGyver and Pete watch from the beach with a SEAL commander as an assault force takes a beach. The SEAL forces come ashore and take out the control center that controls the mines, allowing the marines to land. The commander then explains that they need the Phoenix Foundation to investigate two at-sea robberies that involved SEAL techniques. The military can't become involved in civilian crime so they want Pete and MacGyver to help, and they promptly agree.
Gar Manning and his team of thieves spot a ship bringing up a sunken chest and prepare to move in. Dr. Barbara Ortega and her assistant Paul Engle are opening a chest when Manning and his man Matt come over wearing SCUBA gear. The chest contains Spanish treasure, government papers, and the sunken ship's document box. The log shows the course corrections the ship made that could lead to the entire treasure. Manning and Matt send up an inflatable signal balloon and Ortega and her people spot it and figure it means a diver is in trouble. As they try to haul it up, the thieves come aboard and hold them at gunpoint, and then take the treasure. They have their man Jack bring the boat over, load the chest on board, and sabotage the radio before leaving. Dr. Ortega tries to see them clearly enough to identify them but the pirates shoot, forcing her to keep her head down.
Pete sets up a meeting between MacGyver and Dr. Ortega at her research facility. He goes over everything she reported to the police and notices that only her own crew knew about their find.
At a boatyard, Gar, Matt, and Jack talk to the owner, Arne Lindquist, to trade in their cigarette boat for a ketch. Gar explains that it's time to dump their cigarette boat after the three robberies and use the ketch to take off. First they have to sell the treasure, and Gar plans to contact Ortega and secretly get her to appraise it.
Ortega shows MacGyver pieces of gold from other ships they've found, and admits the center needs the money. Gar approaches her as a tourist and asks where one could buy antique coins. After Ortega gives him a few recommendations, Gar leaves and Ortega explains that she plans to fulfill her dead father's dream to return the treasure to its rightful owners, the residents of Spanish-America. The course corrections in the ship's log would lead to two ships carrying $60 million in treasure. MacGyver notes that the pirates don't know what they have... unaware that Gar is listening in.
At the Foundation, Pete and MacGyver play recordings of various ship engines to see if Ortega can identify what she heard. She finally identifies the correct ship.
Gar and his men are holed up at a motel and packing away the treasure. Their leader explains what he overheard and tells them to watch Ortega and see where she goes. Then they can abduct her and force her to help them get to the treasure. Gar's partners are concerned about a potential kidnapping charge but give in. The next day, Matt and Jack follow her to the docks where she's running a tour for Spanish-American children injured in war. MacGyver arrives and the children wonder if he's Ortega's boyfriend. As they leave, Ortega explains she put up a reward to try and find the cigarette boat and she got a call from Arne Lindquist. Jack is listening in. Afterward, Gar and the others go to Arne's boatyard and confront him. Gar stabs and kills him and they collect their boat, and then wait for Ortega.
At the Foundation that night, MacGyver starts checking cigarette boats registered in the bay. A call comes in from Ortega: it's Jack, impersonating Arne. He tells her to come to the boatyard in an hour and agrees to let her bring MacGyver. They arrive and Jack ushers them inside. Gar and Matt come out and MacGyver recognizes him from the center. MacGyver blinds them by using a blower to spray packing pellets at them, and then gets Ortega outside. He draws them away while Ortega runs to the jeep to get help. However, she can't get it started and Gar captures her before she can get away. MacGyver takes refuge in an old boat but can't get the engine to start. MacGyver tosses a gas can overboard and then hides in the ship. Gar arrives with Ortega and MacGyver knocks a can loose. They realize they've been tricked and lock MacGyver in, and then Gar blows holes in the hull. They leave in the ketch while MacGyver's ship starts to sink.
With time running out, MacGyver is unable to pry the hatch open. He takes the hose from the bilge pump and feeds it into a bumper, wedges the bumper into the hatch, and pumps water into it to try and burst the hatch open. However, the bumper cracks open. MacGyver finds a tank of compressed gas and knocks off the valve, sending it through the hatch. MacGyver swims to the surface. The next morning, they try to locate the ketch without success while determining that Manning is a rejected SEAL candidate who is trying to make the SEALs look bad. They find an island in the area used for naval target practice and covered with unexploded missiles, and figure that a risktaker like Manning would use it. The SEAL commander can't help them officially and advises them to forget it.
Pete takes a boat near the island and drops off MacGyver, wearing SCUBA gear and a transmitter to send a signal when he's rescued Ortega and got her off the island so Pete can call in the authorities. Matt watches from the island but assumes it's a fishing boat. He reports to Manning, who checks in with Ortega to see how she's progressing with the log. He assures her that they'll never look for them in a minefield.
MacGyver abandons his gear and swims ashore. He grabs one missile without setting it off, but it explodes when he tosses it away. Manning figures it's another rabbit setting off a charge. MacGyver heads for the abandoned artillery bunkers but hits a tripwire arming an anti-personnel mine set by Manning. MacGyver ties some string to the tripwire and holds it taut while he slips away. Once he's clear, he releases the string and the mine goes off. However, he ends up falling on another landmine. Manning and his men hear the explosion, realize it's one of the landmines they placed, and Matt and Jack go to investigate.
MacGyver wedges the trigger on the landmine with a twig, and then lifts it clear. He tosses it away but it doesn't explode, and MacGyver realizes it's a dud. He puts it in his pouch and continues. Meanwhile, Jack and Matt split up. Jack comes to a tripwire and freezes, and MacGyver prods him in the back with a stick to convince him he has a gun. MacGyver ties Jack up with his own belt.
At the bunker, Ortega tells Manning that someone is hunting him, and she's close to finding the treasure. Manning assures her that Matt will take care of any intruders.
Matt finds Jack, tied up to brush with a stick stuck to his chest to make it appear he's wounded. He approaches his gagged comrade and MacGyver, hiding in the brush, punches him unconscious. MacGyver ties Matt up as well and heads for the artillery bunker. He places the dud landmine beneath his shirt and approaches the bunker. Inside, Ortega continues to taunt the nervous Manning until he grabs her and takes her outside. MacGyver is on top of the bunker and tells Manning to surrender. He threatens him with the landmine and tosses it to him. When Manning catches it, MacGyver tells him not to drop it. Manning freezes and MacGyver punches him unconscious.
Later, MacGyver is playing soccer at the Foundation with Ortega and one of the injured children, Christobel. MacGyver informs them that Pete is supplying a large dive boat and the grateful SEALs are donating 83 divers to help Ortega bring up the treasure and help the children.