A man wants to testify against his mobster brother in Federal Court, and MacGyver has the job of keeping him safe, but the man's mother is dying and he wants to visit her.

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.

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.

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.