Revenge is what is in store for MacGyver when a master-of-disguise hit man, who MacGyver thought long dead, shows up. This causes MacGyver to flashback to their first encounter.
MacGyver takes a group of Phoenix Foundation employees for a recreational trip into the wilderness but learns that someone of the group might be an escaped criminal.
MacGyver and his grandfather have plans to go to a hockey game. However, when they stop by the Phoenix Foundation to get the tickets, they discover terrorists attempting to blow up a bomb.
An old mentor of MacGyver's asks him to judge a physics competition. The mentor's son becomes despondent after failing to win the competition and locks himself in the lab with a homemade bomb.
Murdoc enlists MacGyver's help to rescue his sister from his former employer. She is scheduled to be executed during a Halloween Party put on by the professional assassination organization.
A cruise ship is the target of a terrorist attack and has three bombs hidden aboard. MacGyver and a friend from the agency are asked to dismantle the bombs before it's too late for the crew and passengers.
When MacGyver's research into the wildlife around the planned building site of a marina threatens to cause a shutdown of the project, the owner hires a beautiful woman to persuade MacGyver to change his mind... by any means necessary.