MacGyver and the team are in Malaysia to extract a terrorist groups' money man, Ralph, who holds key intel to an impending attack. But when a man is shot, the mission goes south, and MacGyver must keep Ralph alive in order to learn the terrorists' plans.
Mac and Jack partner with older versions of themselves, a Russian bomb programmer and his estranged handler, to shut down a Soviet-era warhead in Moscow. But when the antiquated computer needed becomes inoperable, Mac must find a way to fix it with only duct tape and wire.
Using only a wrench and rope, MacGyver must diffuse a bomb set near the United Nations by his old nemesis, "The Ghost", a notorious criminal whose work killed his mentor, and track him down before he strikes again.
MacGyver is tasked to go undercover as an inmate in a maximum security prison to break out El Noche, a notorious drug kingpin, using only batteries and salt, and track him to his cartel's secret location and dismantle it.
Using a screwdriver and bug spray, MacGyver must find the U.S. government mole who is leaking classified intel to the organization that is trying to take down The Phoenix Foundation. Also, Sarah returns to help with the mission, and Nikki reappears, but Mac can't tell which side she's on.
On the way back from capturing a war criminal, Mac and Jack's helicopter crashes in a remote area of Kazakhstan, injuring their pilot and allowing their prisoner to escape with Jack's gun. Using a large blade and a water bottle, MacGyver must get help as the pilot's condition worsens and before the war criminal takes them as prisoners.