A pilot flies Pete and MacGyver over the border of Thailand and into the neighboring country of Nakadebi toward a monastery. As they go, Pete notes that it'll be tough for MacGyver to meet his old flame Debra, and that Pete hasn't seen Sister Margaret for years as well.
At the monastery, a local man, Kahn, brings Sister Margaret word that soldiers are coming for Sister Margaret and Debra. The two women get the children together and hide them in a secret cave beneath the monastery. Kahn offers to delay the soldiers as long as possible, saying he has nothing more to live for.
Pete tells the pilot to drop them as close as possible and meet them in two hours for pickup. Upon arrival, the two men rappel down a cliff and head for the monastery. However, then they arrive at the bottom of the cliff, soldiers open fire on them and they're forced to run for it.
The local commander, Chanthara, arrives and confronts Kahn. When the older man refuses to tell him where the American women are, Chanthara guns him down and sends his men to search the area. MacGyver and Pete camouflage themselves long enough to get by.
Debra tells Margaret that they have to try and escape before the soldiers find the tunnel. She volunteers to find a way across the border into Thailand and Margaret reluctantly agrees.
MacGyver is forced to grab a soldier passing nearby, only to discover that it's Debra. She tells them Margaret is back at the cave and heads back. As she goes, MacGyver remembers receiving a letter from Debra years ago saying that she had no chance but to leave him. He follows her back to the cave where Margaret making sure the children eat. Pete and Margaret have a happy reunion and he assures her they need to stay in the tunnel until the helicopter returns. MacGyver borrows an old softball from a boy and uses the string core for an alarm and for a fake fuse.
Chanthara refuses to give up the search, warning his lieutenant that headquarters will have them both shot if they fail to find the American women. The soldiers check in to report that there's no sign of the women and Chanthara realizes that they must still be somewhere in the vicinity.
MacGyver ties the string to the monastery door to the tunnel. Debra explains that Margaret stopped a soldier from beating a man to death, and Chanthara ordered her execution. Debra insisted on helping as well and ended up on the army's hit list.
Up above, Chanthara spots a worn off sole from a shoe near the concealed entrance. He discovers that the stone slab moves. When he shifts it, it sets off MacGyver's alarm. Pete gets everyone out while MacGyver lights the fuse and runs. Chanthara quickly realizes it's a trick and goes down the tunnel after the fugitives. They head for the helicopter and everyone gets on board. As the pilot lifts off, the soldiers arrive and open fire, puncturing a fuel tank. The pilot is hit and Debra falls out. MacGyver leaps out and Pete calls "Bulgaria." As they flee into the woods, MacGyver explains that "Bulgaria" is a signal meaning Pete will return to the clearing in eight hours.
The helicopter makes it to the refugee camp but the pilot can't control the landing due to his wound. They come down hard but everyone survives. They get out and Pete manages to put the fire out before it explodes. The head of the camp, Gilbert Arnaud, introduces himself and makes sure the children are okay.
As they move through the woods, Debra notes that it's MacGyver's fault she became involved with Margaret. Meanwhile, Chanthara manages to track MacGyver despite his delaying tactics.
Gilbert takes care of the pilot's leg and Pete tells him that he needs someone who can fix the chopper by six p.m. He offers to call someone for Pete but discovers that no one is available.
Debra needs a breather and MacGyver rigs saplings to throw rocks far enough away to draw the soldiers' attention, using Debra's rosary to focus light and burn through the string as a timer. MacGyver briefly studies Debra and strokes her face, but she says it's time to leave.
At the camp, Pete notes an old truck but Gilbert warns that it's not in very good shape. Margaret proposes that they fix the chopper itself, saying she's dealt with broken machinery before and they don't have a choice.
As the soldiers pass the saplings, the rosary fuse burns through the string, throwing the rocks near the soldiers. They open fire and Chanthara realizes where the rocks came from. He finds the rosary and realizes that MacGyver tried to trick them while he heads back for the stream. They head for the stream, unaware that MacGyver and Debra are hiding in the trees nearby. MacGyver figures that Chanthara will soon realize he was distracted. As they head back to the clearing, MacGyver asks Debra why she left. She explains that she figured he was going to ask her to marry him eight years ago, and she wasn't ready for it. MacGyver insists that he was ready. They start to kiss, unaware that a soldier has spotted them. Debra finally says that she's planning on becoming a nun. MacGyver stares at her in shock as the soldier opens fire. He pulls Debra down and they run, while Chanthara and his men arrive and give pursuit.
Pete and Margaret continue to work on the helicopter. She admits that Pete always shows up when she needs him the most. They complete the repairs and go to get the pilot. He tries to start the engine but discovers that the igniter is missing. Pete and Margaret are sure that it was there before.
MacGyver and Debra get back to the clearing. They keep moving around the edge but the soldiers surround and capture them. Chanthara takes them back to the monastery. MacGyver and Debra wonder how Chanthara knew they were heading for the clearing. He locks them up in an old kitchen and tells them that at noon the next day, the villagers will witness their execution.
Pete realizes something in the camp is seriously wrong. They split up to look for the igniter.
MacGyver examines the chimney but realizes it's too small for them to escape. Debra figures they're doomed and talks about what she learned at the convent. She wants to serve God but MacGyver's arrival has turned everything upside down. Debra wonders if she wants children, and is having feelings that she trained herself not to have. MacGyver insists they'll escape and tells her she'll have to decide, and that she should go by her feelings. Debra says that it won't work, that he can't stay in one place. MacGyver insists he'd change for her, and admits he never thought he'd say it.
That night, Debra yells for help. A guard comes in and finds MacGyver seemingly dead, hanging from the ceiling. MacGyver kicks him and Debra knocks the man out from behind. Now they have to wait for Pete to make the next rendezvous.
Pete searches Gilbert's office and finds the igniter. When Gilbert comes in, Pete hides in the shadows. The Frenchman takes out a hidden radio and calls Chanthara, telling him that Pete will be coming to rescue MacGyver and Debra and that he wants his payment. Once he disconnects, he discovers the igniter is missing. Pete walks up and knocks him out, then ties him up. The next morning, he insists on going despite the fact that Chanthara knows he's coming. Margaret insists on going as well but Pete tells her the kids need her. He explains that if things were different, they would have been something special. He says he wouldn't mind a second chance, but Margaret points out that they both would make the same choice. Pete kisses her hand and then leaves in the helicopter.
Chanthara discovers the unconscious guard and the missing prisoners. Once he takes his men to the clearing, MacGyver and Debra emerge from hiding. MacGyver figures they need a way to send a flare to Pete to redirect them to the monastery. He strips the wire from a broom handle to use as a saw. He cuts off a piece of bamboo from a shelf support and pours fertilizer inside, making a crude flare rocket. While Chanthara waits at the clearing, MacGyver adds a funnel as a nose cone.
Pete arrives at the clearing and Chanthara's men open fire. MacGyver hears the helicopter and fires the flare up through the chimney. Pete sees the signal and they head for the monastery. Chanthara realizes they've been tricked and leads his men back to the monastery. The helicopter gets there first and drops a rope ladder so that MacGyver and Debra can hang on as they're lifted to safety.
Later at the camp, Pete assures MacGyver that Gilbert has been taken into custody and Margaret will run the camp. MacGyver gives a new softball back to the boy from the orphanage as well as a baseball glove. He then talks to Debra and tells her he's booked a seat for her back to the States. She tells him that she's decided and will keep her commitment to God. She gives MacGyver a friendly kiss and assures him that he'll always be with her. As they embrace, Pete tells Margaret he'll see her the next time they're in trouble. The two men walk away and they both admit they'll never meet women like them again.