In Lake Como, Italy we see Macgyver, Jack Dalton and Nikki Carpenter (Tracy Spiridakos) crash a party trying to recover a weapon using his handkerchief he grabs some soot from a car to use in order to get the seller of the weapons fingerprint from a wine glass. Using a AA from a stud finder and striped wire to creates a electromagnet to move the guard from the door at the vault he sees a full hand scanner using plaster dust to fool the scanner he takes the canister and returns to the truck to find that Nikki has been captured by John Kendrick (Vinnie Jones) Mac gives him the canister but he shoots Nikki and Mac
Three months after the shooting Thornton visits Mac showing him a video of the virus in action. At DXS (department of external services) they hit a wall on Nikki's computer, so Jack brings in Riley to bypass the wall to show John and Benjamin Chen in San Francisco.
In San Francisco Mac uses a corrosive agent, Ammonia, and aluminum to create smoke in order to draw out Kendrick he sees Nikki with. Kendrick tells them that he shot Nikki with a blank so that she could disappear under the alias Eliza Pittsinger. At the airfield, they stop Nikki from taking off, but she already sold the weapon. Nikki tells them where Chen is Mac disables the canister from the I.E.D using the canvas top as a parachute. Thornton tells Mac and the others that DXS is shutting down but are going under as a new name which Mac crosses as Phoenix. While is police custody Nikki escapes.
In North Korea, Mac and Jack transport an asset to South Korea. Riley using boxer as a fake boyfriend to get her p.o. off her case. Mac searches through Nikki's apartment looking for anything to help them find her when Jack walks in they get a call saying they have a new mission to rescue a spy by the name of Sarah Adler (Amy Acker) from Jacks past who is in Venezuela to confirm that Alfredo Barrios are now running his operation from Caracas which is confirmed. Jack has a flash back of him and Sarah in Belarus.
Jacks contact Julio tells them where to find Sarah. Using a car battery, cupro-nickel and jumper cable Mac build an arc welder to get into the building. Building a set of night vision goggles macgyver rescues, Sarah.
At her apartment she finds Luis dead, she hands Mac a flash drive with the ledger info on it and tells them that she is going after barrios. Using an old school modem Riley sends the ledger info to Thornton while Mac, Sarah, and Jack sneak onto barrios compound. Thornton rescues Riley before the police take her. Following barrios, Mac uses netting and some wrenches to send him flying. Back home the team in introduced to Sarah's fiance. Macgyver is back at Nikki's apartment where he finds a passport under the name Alice Hunter in an electrical outlet.
In Somalia, jack and Mac are in a burning building to take out a chemical weapon factory. Mac uses the liquid foam from the fire extinguishers and body bags to safely land when they drop from a high window.
Talking to his dead dad Jack tells him about his latest adventure. Their latest mission is to take down d-77 in order to do that they need Ralph castrati (Oliver Cooper) the gang's accountant in Labuan Malaysia. In the van outside Ralph's place Mac makes a directional antenna with a soda can and Wi-Fi chips to disrupt the alarm signal to get the code. Once they have Ralph he gets shot by a sniper Riley goes to get a doctor. Using jacks license as a makeshift cover Mac can keep him alive until he has time to do an intercostal chest drain.
Riley creates a distraction so that they can sneak Ralph past a receptionist. Using office supplies, Mac can fool d-77 that Ralph is dead but the gang takes his body to make sure Mac can rescue him using soda bottles, and rubber tubes for mask and a gas cap canister to create smoke he can give him the antidote in time. Mac writes his father a letter hoping to reconnect with him.
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