While testing a new nuclear bomb defusing team at the Phoenix Foundation, a deadly explosion kills three men. Pete blames himself for not inspecting their equipment better and resigns from his job out of guilt. However, Pete is replaced by a not-so-trustworthy man—one who may have been connected to the explosion.

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.