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."

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 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 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.

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.

Dalton, who is believed to be dead, recruits MacGyver to help uncover a CIA mole.

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.