When a science lab studying the ozone layer mysteriously explodes, MacGyver is called in to rescue the scientists that are trapped underground. It's soon discovered that the explosion cracked a tank of sulfuric acid, and MacGyver is in a race against time before the Army uses a missile to seal up the base.

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.