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 unhappy 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 a shocking secret to the team: she has a husband who's been undercover in a criminal organization called D-Company 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 hit the road for a weekend of relaxation in Las Vegas, but their mini-vacation is cut short when someone from their past abducts them and locks them in a concrete room.
The Phoenix teams up with a woman who's a soccer mom by day but a master thief by night to catch one of her contacts, an underworld criminal, who has hired her to steal a dirty bomb.
When MacGyver takes Riley and Bozer into the wilderness for a weekend of survival training, things take a turn when they run into a unhappy group of criminals who are searching the rugged backcountry for a lost crate of money. Also, Jack and Matty go on a road trip to place Matty's ex-husband and his family in witness protection.
An international crime boss offers Matty a deal she can't refuse - he'll surrender himself into her custody if he's allowed to return to the United States to watch his daughter walk down the aisle. MacGyver and team crash the wedding to ensure the crime lord doesn't run, only to discover they're not the only ones lying in wait at the event.
After a surprising introduction to Phoenix's newest recruit, Desi, MacGyver and 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
MacGyver and team are asked to solve a locked-door mystery when a man working inside a remote, ultra-secure international seed vault disappears.
When Nicholas Helman resurfaces to carry out a killing spree, the team is forced to get help from the one person who knows him best- his protege, Murdoc.
MacGyver and Desi help a group of Syrian refugees who are being pursued by human traffickers. Also, in Los Angeles, Bozer is trapped in Oversight's car which is rigged to explode.
When two American tourists go missing while doing a "No-Go Scavenger Hunt" through some of the world's most dangerous countries, the Phoenix team goes undercover as backpackers to find them and bring them home alive.
Matty's ex-husband, Ethan, asks her for help when a criminal organization, S-Company, kidnaps his wife and daughter, forcing Matty to decide if she's willing to commit treason in order to help him save his family. Also, Riley joins Billy Colton and Mama Colton on a mission to Paris and makes a heartbreaking discovery.
MacGyver faces off with a cunning new adversary whose carefully crafted plans put Mac at the epicenter of an impossible choice: save the life of a friend, or save the lives of hundreds of innocents. Also, Mac receives new information that will drive a wedge between him and his father.