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."
Mac inadvertently leads a hit man to his target, believing that he's helping a father find his lost son.
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
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 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.
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 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.
While hang gliding in the west, MacGyver crosses paths with an escaped felon who shot and wounded a rare eagle. Now, with the help of his new friend Susan Cooper and her son Darin, MacGyver must heal the eagle and trap the felon before he kills more eagles.
While helping the Phoenix Foundation test a new missile-guidance system for the government, MacGyver's efforts are hampered by men who are trying to steal it. When the men escape with it, MacGyver turns to his deaf friend, who has been having premonition-type dreams of this happening. Now MacGyver must try and analyze her dreams so that he can find the men who stole the system.
A retired actor and his wife stop at a motel on the way to Los Angeles. MacGyver rescues them from a drunkard who nearly makes a mark on their car.
MacGyver is supposed to meet a mobster-turned-informant at the motel, but the meeting goes wrong. The mob shows up and kills MacGyver's friend before he can give MacGyver what he promised. Instead the bag lands in the old couple's car, where the old actor finds it and discovers it full of money.
While retrieving tickets for a hockey game at the Phoenix Foundation, MacGyver and his grandpa Harry get caught in the middle of a woman's plot to blow up the building using a bomb that she herself made. They try to escape, but are locked in. Now they must figure another way out before she activates the bomb.
Pete's ex-wife and son are kidnapped down in Louisiana while on an archaeological trip. The kidnappers demand that Pete comes to Louisiana in exchange for letting his family go. But when he gets there, it soon becomes apparent that they don't plan to let any of them go.
MacGyver puts up Penny Parker for a few days while she's looking for a job as a singing telegram. But on her first day, she happens to witness two thugs torturing a man. Unfortunately, she can't find her way back, and when she does, MacGyver thinks this may be the start of something bigger as the victim is a Federal agent.
MacGyver's fishing trip is cut short when he meets a very pregnant woman whose husband is out to kill her. Accidentally, she found out that his half-way home for ex-cons is really a recruiting place for new crimes. Mac and the woman are chased into a warehouse where they are trapped.
While on an expedition to find a Spanish treasure fleet, Dr. Barbara Ortega's boat is hi-jacked by modern-day pirates. They steal the small amount of treasure that she has already found - including the ship's log, which is the key to finding the whole fleet - and take off. When she makes it public that she was hi-jacked, the Phoenix Foundation sends MacGyver to help. Now, MacGyver and Barbara must recover the ship's log, so she can find the treasure before the pirates do.
When MacGyver and Pete go skiing, a man switches poles with MacGyver, only moments before being gunned down and killed by his former friends. But the gunshot starts an avalanche, which covers MacGyver completely, leaving it up to Pete to convince the mountain rangers to stage a search and rescue before the next avalanche comes. As MacGyver finally is dug up, the gangsters are there, waiting for him, and whatever is hidden in that ski pole.
Dalton, who is believed to be dead, recruits MacGyver to help uncover a CIA mole.
MacGyver and Pete meet at a wrecking yard, both thinking that the other one arranged the meeting. Soon an unknown assailant captures them inside a big truck. Their only clue is an obituary for them and Jack Dalton.
When MacGyver is sent to rescue an American pilot held in Central America for supposed espionage, his wargame-trained daughter tags along, but she didn't quite come prepared for the real thing. MacGyver must now rescue the pilot while keeping his daughter safe from the soldiers.
MacGyver's friends throw a birthday party for him, but he's somberly reflecting on his past and future. While reflecting, MacGyver decides to leave the Phoenix Foundation to get married and have a family. Can Pete convince him of how important he is to the Foundation and get him to change his mind?
MacGyver is called to a meeting with a former British spy, who has learned of a group of terrorists that will use a new plastic explosive in a vengeful attack on the U.S. army. This explosive can be hidden anywhere. However, before the spy can give MacGyver all the details he is shot. MacGyver flees through a window and is picked up by a boat. The female who owns the boat soon learns that the man she has rescued doesn't have any memory.
MacGyver is forced to work with a ruthless freelance agent to rescue a human rights activist who is being held in a psychiatric hospital in Czechoslovakia. The rescue is an apparent success, until the secret police then kidnap the activist's wife to get him back.