MacGyver and Pete have a pilot fly them over the border separating Thailand from neighboring Nakadebi. They're heading for a monastery serving as an orphanage to save two old friends: Sister Margaret and MacGyver's old flame Debra Easton.
At the orphanage, a local villager, Kahn, warns Sister Margaret that Captain Chanthara and his men are coming to arrest them. Kahn volunteers to delay Chanthara while Sister Margaret and Debra hide the children in a secret tunnel beneath a stone platform in the center of the courtyard. He insists that he's an old man and he will use what little time he has left to save the women and children.
The pilot drops Pete and MacGyver off as close as possible to the orphanage, and promises to return in two hours. The two men rappel down a cliff but Chanthara's men spot them and open fire. The men play a game of cat-and-mouse, evading the soldiers while working their way toward the orphanage.
Chanthara and his men arrive at the orphanage and Kahn refuses to tell them where the women and orphans are. Chanthara shoots him down and orders his men to search the orphanage. Below in the tunnel, Debra tells Margaret that Chanthara will eventually find the tunnel and they have to escape. She leaves the tunnel to find a route to the Thailand border.
MacGyver and Pete hide in the jungle and MacGyver grabs a passing soldier. He discovers it's Debra, who leads them back to the tunnel. As they go, MacGyver remembers receiving a goodbye letter from her years ago, saying that she had to leave. They arrive at the tunnel and Pete and Sister Margaret are reunited. MacGyver borrows an old softball from a boy and unweaves the string core, then uses the string to rig an alarm system to the stone slab concealing the orphanage entrance. He douses the rest of the string in kerosene and animal fat and lays it down as a fake fuse, figuring Chanthara won't know any better. He wonders why the Chanthara wants the women and Debra explains that Margaret stop a soldier from beating a villager to death, and Debra became involved as well.
Chanthara is aware that his superiors will have him executed if he doesn't find the women. He's sure that the fugitives couldn't have gotten far with all the roads blocked. Chanthara spots the sole of an orphan's shoe near the stone platform and realizes it conceals a tunnel below. When he opens it, the alarm goes off and Pete and MacGyver quickly evacuate everyone out of the tunnel. MacGyver lights the fake fuse but it only delays the canny Chanthara for a few seconds. Everyone heads for the clearing where the helicopter is scheduled to land. The pilot arrives and they load up, but the soldiers open fire as the helicopter lifts off. One shot punctures the fuel tank and another one hits the pilot in the leg. He loses control and Debra is thrown out. MacGyver jumps after her as Pete yells "Bulgaria!" As MacGyver and Debra run into the jungle, he explains that "Bulgaria" is a code sign meaning that Pete will come back for a rescue every eight hours.
The helicopter makes it to a refugee camp in Thailand but the pilot loses control. They manage to land safely without the helicopter exploding. The camp supervisor, a Frenchman named Gilbert Arnaud, greets them and finds quarters for the orphans.
MacGyver and Debra move through the jungle, buying time until Pete can return. They go through a stream and MacGyver attempts an old Cherokee trick: walking backwards into the stream and then walking downstream. However, Chanthara has watched old Western movies and quickly catches on.
Gilbert gets medical treatment for the pilot and assures Pete that he'll find someone to pilot the helicopter so Pete can return to the rendezvous at 6 p.m. However, Gilbert is unable to find a pilot in time.
Debra starts to get winded, and they pause for a breather. MacGyver makes a crude catapult out of saplings and vines, loads it with rocks, and sets a string as a trigger. He then uses Debra's rosary and lines it up so the sunlight will hit it in a few minutes and burn through the string. MacGyver looks affectionately at Debra and she starts to respond, but then says they have to go.
At the refugee camp, Pete is unable to find any other form of transportation to get back to the clearing. Margaret says they need to work on the helicopter engine themselves, and they go to work.
Chanthara and his men pass the saplings, which fire the rocks on queue. The soldiers fire at the noise as the rocks slam down, but Chanthara realizes it's another trick to draw them away from the stream. He leads his men back there, unaware that MacGyver and Debra are hiding in a nearby tree. Once the soldiers are gone, MacGyver and Debra head for the clearing to make their 6 p.m. rendezvous. As they go, MacGyver finally asks Debra why she left and she explains that she knew he was going to propose and she wasn't ready. MacGyver says that he was ready and starts to kiss her. Debra starts to respond, but then says she is becoming a nun. Before a startled MacGyver can respond, a sniper spots them and opens fire. They duck for cover and then run for the clearing.
As Pete and Margaret work on the helicopter, Margaret observes that Pete always shows up just when she needs him most. They share a quiet moment and then finish the repairs. The pilot confirms that their work is good but the igniter is missing, despite the fact Pete and Margaret saw it earlier.
MacGyver and Debra return to the clearing, but Chanthara is waiting for them and takes them back to the orphanage. As they wonder how he knew they'd be going back for the helicopter, the captain locks them up in an old kitchen and tells them they'll be executed the next day at high noon.
Pete figures something suspicious is going on and he and Margaret split up to look for the igniter.
MacGyver checks the chimney but it's too small for them to crawl out. Debra explains that she wants to serve God but now MacGyver's arrival has challenged her resolve. She admits that since she's been working with children, she's been wondering if she wants to have some but notes that the church frowns upon married nuns. MacGyver assures her that they'll escape but that she'll need to make a decision and tells her to go by her feelings. Debra considers the matter and then says that it would never work because MacGyver can never stay in one place. He tells her that he would for her, even though he never thought he could do it.
That night, a guard investigates when Debra yells for help. MacGyver is hanging from the ceiling by his neck, seemingly dead. When the guard approaches him, MacGyver kicks him and Debra clubs him unconscious from behind. MacGyver frees himself from his makeshift harness and they prepare to wait the night until the next scheduled rendezvous.
Pete searches Gilbert's office and finds the igniter hidden away. When he hears Gilbert coming, Pete hides in the shadows and listens as the supervisor calls Chanthara on a hidden radio and tells him about the next rescue attempt. Pete knocks him out and the next morning tells Margaret that he's going even though Chanthara knows he's coming. Margaret wants to come but Pete says that the orphans need her well. He talks of how they might have had something together and wishes they had a second chance, but Margaret assures him that they both would have made the choices and they'd still be in the same place. Pete gently kisses her hand and then leaves in the helicopter.
At the orphanage, Chanthara discovers the unconscious guard and realizes the prisoners are missing. He figures they're heading for the clearing and goes in pursuit. Once he's gone, MacGyver and Debra emerge from hiding and try to come up with a way to tell Pete where they really are. MacGyver makes a crude flare out of a piece of bamboo and fertilizer. When Pete arrives, MacGyver hears the engine and fires the flare up through the chimney. Pete sees it and flies to the orphanage, drops a rope ladder, and carries MacGyver and Debra away before Chanthara can return to stop them.
Later, Pete tells MacGyver that Gilbert has been arrested, and Margaret is the new camp supervisor. MacGyver replaces the boy's softball with a new one and a baseball glove. He then tells Debra that he's booked her a seat on a plane back to the U.S. She tells him that she'll be staying to run the orphanage and keep her commitment to God. She gives MacGyver a friendly goodbye kiss and tells him that he'll always be in her thoughts. Meanwhile, Pete and Margaret share a farewell hug and he promises that he'll be there for her whenever she's in trouble. Margaret says she'll be looking forward to it. As the two men walk away, they both agree that they'll never meet women like Debra and Margaret again.