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MacGyver and Pete head to Asia to rescue a nun, who is an old friend of Pete's, and the orphaned children she takes care of from aggressive regime troops. While there, MacGyver runs into someone he never expected, his old fiancee, Debra. Now MacGyver must complete his mission, work out his differences with Debra, and escape from the troops, all before the troops find them.

MacGyver, returning home one night, walks into his apartment, only to everything he owns missing from his apartment. Initially suspecting a robbery, MacGyver eventually comes to the conclusion that his old friend Jack Dalton is the one responsible for the theft.

MacGyver goes to the mountains to lead four ex-gangster teens on a Phoenix Foundation funded rehabilitation trip. When he gets there, he finds that this task may be a little more complicated then he thought. All of the kids are very rebellious and one of them has a bad grudge against another one. A couple of days later when MacGyver is returning with the kids, their plane crashes in the middle of the wilderness and one of them is injured. Now, MacGyver must fix the plane and help the kids work out their differences so they can save their friend.

While MacGyver goes to pick up a Chinese friend's brother from a birthday party, he witnesses something strange: Paul is being called "The Wish Child." It seems that a greedy businessman has wrapped him up in a scam, because he looks exactly like a boy from an old legend that owns the secret of immortality. Now, MacGyver must try to talk him out of this, because Paul is starting to believe he really is The Wish Child!

MacGyver and Pete have a surprise party planned for a colleague, but when the colleague doesn't show up, MacGyver goes looking for him, and finds him on the verge of committing suicide. When questioned why he would do such a thing, Kelly explains that a con artist has swindled him out of his life savings. MacGyver tells Pete about Kelly's situation and the two of them decide that they will get Kelly's money back from the con

Mac inadvertently leads a hit man to his target, believing that he's helping a father find his lost son.

MacGyver and Pete are testing a new security system at the Strategic Research Development Administration. MacGyver successfully bypasses the security and meets Dr. Jill Ludlam, the system's designer. She tries to turn off the security system, but it doesn't realize that it was just a test. MacGyver and Dr. Ludlam are then forced to find a way out, as the security system, named Sandy, tries to destroy the "intruders."

Posing as a watchmaker who manufactures bomb timers, MacGyver manages to catch a master killer—Piedra—before he attempts an assassination on a high-profile target. However, Piedra isn't about to be stopped for long.

Pete Thornton investigates the supposed death of an old friend, a prominent Russian dissident, and finds he must get his friend's daughter Maria out of the country before the secret police arrest her for an alleged conspiracy. However, while in Russia, Pete bumps into MacGyver, who followed him from the United States. While disappointed MacGyver followed him, Pete gladly welcomes MacGyver into his plans when the secret police arrive to take Maria into custody. Following a high speed boat chase to escape the police, Pete and MacGyver find out from Maria that her father is not dead, he is being held in a maximum security ward at a state mental institution. To get into the mental hospital, MacGyver plays the part of a mad patient and Pete plays the part of a doctor who has been assigned to him. With the help of the other patients, MacGyver is able to escape into Ward Zero, where Pete's friend is held. MacGyver breaks him out and hides him with the other patients

When a mother superior at a religious mission in North Africa asks MacGyver to help a young woman with something, he is glad to help. However, when he finds out the young woman wants him to break her brother out of jail, he may have taken on more than he expected.