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.
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.
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.
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.
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.
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 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.
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 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
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."