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.

After MacGyver witnesses someone dumping toxic waste that's polluting mountain streams, he and Pete enlist a reclusive mountain man nicknamed "Earthquake" to help lead them to the culprit. Things become complicated, though, as Earthquake's flashbacks to his military service in the Vietnam War make him unstable and threaten their case.

Mac and Jack return from a flight to find an abandoned baby in Jack's hangar, complete with a desperate note from the mother and his own endowment fund hidden in his diapers.

Penny Parker's big chance in a major professional role is threatened from two directions: a money shortage and several deaths linked to the musical she is set to perform in.