MacGyver attempts to get a reporter out of a Central American country with evidence linking a general to an illegal arms dealer. As they reach the border, it is clear escaping to Mexico will be no easy task, as the general and the arms dealer have every imaginable route severely guarded.

MacGyver comes along on a expedition to Brazil with his friend, entomologist Dr. Alden. They meet with a landowner and recluse, Trumbo, who is initially hostile. However, when they realize that a mile-wide column of army ants is moving through the jungle, they team together to mount a defense.

MacGyver is trapped in a mansion with Pete, a code expert, and a government agent who may or may not be on their side. However, an old nemesis has electronically booby-trapped the entire mansion to make sure they can't go anywhere.

An old girlfriend of MacGyver's contacts him for help after she discovers evidence of uranium thefts from a nuclear processing plant where she works.

At the beginning of the episode, MacGyver literally has to jump onto a moving train that he missed earlier to return top-secret files and documents to the U.S. Government. Soon after, a local tribe stops the train. They take all passengers hostage until the men responsible for the death of the tribal leader's son is found among the passengers.

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.

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.

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!

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.

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.

While mapping the wilderness for the Phoenix foundation, MacGyver stumbles on a deserted ship and finds a runaway girl who tells him that the rest of crew was driven away by Bigfoot.

After returning home from a long assignment, MacGyver has an unwelcome surprise. Jack Dalton is waiting and wants him to help with a new scheme. A wealthy woman has just acquired some invaluable jewels, needing Jack to fly her back to her home in France. Things seem to be going fine, that is, until they land. Jack and MacGyver are arrested and accused of theft.

After MacGyver witnesses someone dumping toxic waste that's polluting mountain streams, he and Pete enlist a reclusive mountain man nicknamed "Earthquake" to help lead them to the culprit. Things become complicated, though, as Earthquake's flashbacks to his military service in the Vietnam War make him unstable and threaten their case.

Exhausted MacGyver dreams he's a Civil War vet trying to claim a home in Montana that's threatened by a neighboring rancher who looks a lot like Pete Thornton. But this Pete has hired Murdoc to kill Mac...