Murdoc moves ahead with his plans for revenge against MacGyver by recruiting his recently released former cellmate to infiltrate the Phoenix Complex and kill every agent inside.
When the team intercepts a terror group’s message for Murdoc, instructing him to kill a tech analyst, Mac poses as a psychopath to save the intended victim.
Mac’s close friend from M.I.T. fakes her own death to prevent someone from killing her in order to suppress her scientific research.
After an earthquake in Hawaii, Mac and the team join Chin and Kono from the Five-0 task force to rescue a group of government scientists trapped in a building; another group tries to steal top-secret weaponry from the scientists.
When Mac and the team are blamed for a terrorist bombing, the Phoenix Foundation is forced to disavow them; the team must clear their names without support from back home.
Mac and Jack must track down a corrupt FBI agent who has framed a man for murder; everyone on the team is terrified to get a performance review from the tough new boss.