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 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.

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.

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 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.

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?