Three months after quitting the Phoenix Foundation and moving to Nigeria, Mac puts aside his differences with his father and returns when he hears Jack is the target of a murderous dictator he double-crossed.
When Jack receives an emergency distress signal from one of his old Delta buddies who is falsely accused of terrorism in a foreign country, MacGyver and Jack quickly recruit the rest of Jack’s old Delta team and stage an unsanctioned rescue op.
MacGyver, Riley, Bozer and Leanna go undercover on a college campus to smoke out a deep-cover operative who is recruiting students to carry out deadly attacks around the world. Also, Jack joins bounty hunter Billy Colton in the hunt for a bail jumper but is concerned when he finds out Billy offered Riley a job.
MacGyver and Riley, with the help of Vasil, a distraught father, must find a way to drive a tanker filled with liquid oxygen through a region occupied by rebels and deliver it to a children’s hospital before they run out. Also, Riley helps MacGyver decide whether or not to allow his father back into his life.
When Oversight’s attempt to capture a drug cartel’s leader goes bad, MacGyver and Jack rush to Mexico to pull their boss out while racing through the heart of the country during Dia de Muertos celebrations. Also, Bozer and Riley use Halloween as a distraction to gather intel on a man accused of treason.
Murdoc abducts MacGyver’s girlfriend, Nasha, to force Mac to help him rescue his son, Cassian, from a kidnapper. Also, a dangerous individual from Murdoc’s personal life shows up, giving Mac a glimpse into the villain’s past.
Matty sends MacGyver and team to Ghana to recover a hard drive from an e-waste landfill that is run by a powerful and violent man. But when Matty refuses to reveal what’s on the drive, other than a mysterious file called “Dragonfly,” the team speculates about what could be so important to her.
MacGyver and the team set off on a dangerous capture operation after an Irish military intelligence officer approaches them claiming to know the whereabouts of “The Ghost,” a lethal bomb maker whom Mac has been hunting for years.
When a vial containing a deadly virus is stolen from the Center for Disease Control in Atlanta, MacGvyer and team race to recover it before the thief unleashes a global pandemic.
Matty reveals the shocking secret that her husband has been undercover in a criminal organization for eight years; when his status as a CIA agent comes out, Matty needs MacGyver to find and extract her husband before it's too late.
Mac and Jack's mini-vacation is cut short when Griggs from Mac's first mission apart of DXS abducts them and locks them in a concrete room as revenge for leaving him and another agent Hadley in a mission gone wrong in Jakarta. Mac fakes Jack's death to reveal Griggs's identity and knocks him out. Meanwhile, Matty tasks Riley, Bozer and Leanna with stealing a diamond encoded with terrorist intelligence from a princess in Milan. Bozer asks Leanna to move into a new apartment with her as a new stage in their relationship.
Mac and the gang team up with Charlotte Cole, who is a mom by day but a master thief by night, to catch an underworld criminal known as "The Fence". Matty tasks Riley to pretend to be Charlotte Cole in order to find out what task The Fence has in store for Charlotte. The Fence tasks Riley to steal a dirty bomb hidden in a brief case from Silverwall in Moscow. Matty threatens Charlotte to help them to stop the dirty bomb from getting in The Fence's hands, in return for not telling her family about the truth about her activities. There are extensive security measures in which they need Charlotte's help to get through, which The Fence had mentioned that Charlotte had passed through before. The Phoenix team successively infiltrate Silverwall and find the dirty bomb. Mac determines that the bomb is made of Americium 241 and successively defuses it with Charlotte's help. Charlotte double crosses Mac and handcuffs him to the table, getting away with the suitcase. The team find the plane Charlotte is scheduled to fly back in back to Los Angeles in order to hand over to The Fence. In order to stop the bomb getting into a domestic terrorist's hands and exploding on American soil, Riley intercepts the exchange but since Riley was initially pretending to be Charlotte Cole, this forces The Fence to hesitate when they are held at gunpoint. The Fence reveals that he has Charlotte's family in captivity to determine the real Charlotte Cole. With Riley about to be shot, Mac saves her with a flaming tire trick.
Having taken Bozer and Riley to the Washington state wilderness for a survival training session, Mac is captured by a group of criminals. While Riley and Bozer work to locate Mac without the aid of technology, Mac stays alive by assuring the thieves he can locate their stolen crate of cash that was washed away by a storm. Elsewhere, Matty and Jack receive credible evidence that the people Ethan double-crossed while undercover have located him and his family. The two thwart an attack and help Ethan and his family relocate again, but in the process, Ethan's wife Deena learns about his history with Matty. Matty assures Deena that Ethan's life is with her and their child, saying she will not attempt to win him back.
Alonzo Olvera, an international black market arms dealer, offers to turn himself in and provide Matty with details of his operation if she will give him safe entry into the United States to walk his only daughter down the aisle on her wedding day. Matty agrees, but has Mac, Jack, Riley and Bozer pose as wedding guests to make sure Alonzo doesn't try to escape. Armed thugs, thought to be irate arms customers of Alonzo's, storm the wedding reception. After they are captured, Alonzo is found to have been killed via cyanide injection. Mac deduces that a wedding guest, someone very close to Alonzo, is behind the attack. After a successful capture of the perpetrator, Jack tells the group that he is leaving on an open-ended mission to take down international terrorist Tiberius Kovac, whom Jack originally thought was killed in an explosion.
After a surprising introduction to Phoenix’s newest recruit, Desi who is MacGyver's and their team are assigned to escort and protect an ATF (alcohol, tobacco, firearms) gun-sniffing dog who has a bounty on his head, only to discover they’re not the only ones crashing the weapon drop.
The Phoenix must recover the body of a pilot whose plane crashed while testing an experimental laser mapping system that MacGyver designed. Also, Riley tries to identify the hacker who tricked a SWAT team into arresting her and Elwood.
Mac, Riley and Desi head to Greenland, where a man working in a highly secure international seed vault has vanished without a trace. Upon arrival, the team finds a dead body and one packet of seeds missing from a North Korean crate; the seeds being for a pea pod whose plant can by synthesized into a deadly poison. Suspecting a terror plot, the team ultimately locates the escapee, Arthur, only to learn he has a revenge motive instead. At home, Mac has Bozer and Leanna tail his father, suspecting he is hiding something. Mac later finds his dad in a hospital, receiving cancer treatments.
Phoenix learns of a hit that is apparently the work of Nicholas Helman, presumed to have been previously killed by Murdoc. After discovering that Helman has been hired to kill members of a Hong Kong cartel that were planning to turn state's evidence, the team goes to the Phoenix black site to seek Murdoc's help in locating his former mentor. The cartel hits are discovered to be a plot conceived by Murdoc himself, who used his son's visits to breach the black site's security system and lure Helman to him. In a scuffle between Murdoc, Bozer and Helman, both Bozer and Helman are shot while Murdoc escapes. However, Murdoc is later captured by Mac and his father. As additional punishment, Murdoc is forced to share an adjoining cell with Helman, who survived the shooting, as did Bozer.
Out of contact with Phoenix due to their cell phones being lost in a scuffle in Bosnia, Mac and Desi happen upon a truck that has fallen into a sinkhole, trapping a family and a badly injured border guard. While helping the family get out of danger, Mac learns they are Syrian and the border guard was shot by a rogue group trying to keep Syrians out of the country. Back in Los Angeles, Bozer is thrilled that Mac's father is letting him drive his new company vehicle with all the bells and whistles. But upon pressing the brake to start the vehicle, Bozer realizes he's triggered a bomb that will go off if he releases the brake. Riley eventually disables the bomb by hacking into the vehicle's CAN bus, but now Phoenix must try to figure out who wants Oversight killed.
Two American tourists go missing while doing a scavenger hunt through some of the world's most dangerous countries; the Phoenix team goes under cover as backpackers to find them and bring them home alive.
Matty's ex-husband, Ethan, asks her for help when a criminal organization kidnaps his wife and daughter; Matty must decide if she's willing to commit treason to help Ethan; Riley joins Billy Colton and Mama Colton on a mission to Paris.
On April 18, 2018, CBS renewed the series for a third season. Along with reboot series Hawaii Five-0 and freshman series SEAL Team and S.W.A.T..
On November 26, 2018, it reveals that George Eads would exit immediately after three seasons for the release of his contract so he could spend more time with his young daughter who resides in Los Angeles due to filming the series in Atlanta. Producers ultimately agreed with Eads to be written out of the show but leaving the opportunity for him to return as a guest star in the future.
Levy announced that she will recur in all episodes, after Eads departure.
Poll[]
<Poll>
What is the best episode of Season 3?
Improvise
Bravo Lead + Loyalty + Friendship
Bozer + Booze + Back to School
Guts + Fuel + Hope
Dia de Muertos + Sicarios + Family
Murdoc + MacGyver + Murdoc
Scavengers + Hard Drive + Dragonfly
Revenge + Catacombs + Le Fantome
Specimen 234 + PAPR + Outbreak
Matty + Ethan + Fidelity
Mac + Fallout + Jack
Fence + Suitcase + Americium-241
Wilderness + Training + Survival
Father + Bride + Betrayal
K-9 + Smugglers + New Recuit
Lidar + Rogues + Duty
Seeds + Permafrost + Feather
Friends + Enemies + Border
Murdoc + Helman + Hit
No-Go + High-Voltage + Rescue
Treason + Heartbreak + Gum
Mason + Cable + Choices
