Episode #1: "The Rising" September 23, 2016
Angus "Mac" MacGyver, with help from Jack Dalton and Nikki Carpenter (Tracy Spiridakos), infiltrates a party to steal a biological weapon. However, as Mac and Jack meet up with Nikki, they find her held hostage by John Kendrick (Vinnie Jones). Mac gives up the bioweapon, but Kendrick shoots both him and Nikki. Three months later, Nikki is dead and Mac is on holiday when his boss, Patricia Thornton of the Department of External Services (DXS), arrives.
Thornton shows him video of a lab where the bioweapon was used and calls Mac and Jack back in to help. With information stuck on Nikki's hard drive, the two recruit hacker and convict Riley Davis, who tracks Kendrick to San Francisco. The group not only finds Kendrick, but also discovers that Nikki is alive and working with him for another group. After capturing them both, Mac finds out that Nikki has already sold the bioweapon to someone who plans on making it airborne via an IED. Mac finds the bio-weapon and extracts it from the bomb before it explodes.
A few days later, Mac is at home burning photos of Nikki when Jack, Riley, and Thornton come to meet him. Thornton tells the group that Nikki's betrayal has caused knowledge of the DXS to become compromised, so they have to shut down and relocate under a new name of their choosing. Mac chooses the name Phoenix, to which the rest of the group agrees. Elsewhere, Nikki is in handcuffs, being transported by car. After the car goes through an overpass, the driver and passenger discover that Nikki has disappeared, leaving the cuffs behind with a hairpin.
#2 "Metal Saw" - September 30, 2016
In the two weeks since Nikki escaped FBI custody, MacGyver has been going to Nikki's apartment trying to find something that will lead him to her. The team gets an assignment to rescue Sarah Adler (Amy Acker), Jack's former partner and ex-girlfriend from the CIA who has been disavowed due to being captured. Sarah's capture comes on the heels of her stealing an arms dealer's ledger. Together, the team retrieves both Sarah and the ledger while also taking down the dealer. Sarah is reunited with her fiancé. At the end of the episode, Mac finds a secret compartment at Nikki's place containing a passport for her alias. Meanwhile, Riley meets with her parole officer and has Wilt Bozer portray her boyfriend. In exchange, she agrees to give him one digit of her phone number each week.
#3 "Awl" - October 7, 2016
A terrorist group known as D-77 is planning an attack somewhere. The group's financials are managed by a guy named Ralph Kastrati (Oliver Cooper), who is wanted by the FBI for several accounts of securities fraud and lives in Malaysia. The team goes to secretly collect Ralph, who then gets shot by D-77. MacGyver, using items found in Ralph's SUV (including parts of the SUV itself), saves Ralph's life. Later on, in order to prevent D-77 from killing Ralph, MacGyver lowers Ralph's heart rate until his pulse can't be felt, giving him the appearance of death. Before D-77 can actually kill him, however, Mac and Jack rescue Ralph, who willingly testifies about D-77 and will be put in witness protection. At home, Mac acts as the monster for Bozer's movie and Riley helps out with the CGI software. Jack tells Mac to contact his father, as he hasn't talked to him in a long time. Mac decides to write his father a letter.
#4 "Wire Cutter" - October 14, 2016
An agent of the Phoenix Foundation is killed after discovering an old Soviet bomb is being held by Vladimir Sevchenko (Yorgo Constantine), a Russian extremist who wants to restart the Cold War. Riley discovers that the bomb uses its own unique operating system. While Thornton goes to find Sevchenko's whereabouts, the team searches for the programmer behind the bomb's code, a man named Alexander Orlov (Elya Baskin), and his handler who knew the passwords to disable it, Victor Levkin (Olek Krupa). Orlov and Levkin share similar qualities to Mac and Jack, respectively. Orlov uses items near him as unorthodox tools and Levkin keeps multiple handguns on him at all times. The group goes to Russia to collect an old computer needed to interface with the bomb, but Orlov is kidnapped by Sevchenko's men in the process. The group meets with Thornton to save Orlov, but the computer's keyboard is damaged and Levkin is mortally wounded. Mac wires objects to the keys so that, when an object is tapped, the computer thinks it's a keystroke. The bomb is deactivated and Sevchenko is defeated. Orlov is thanked and returned to his retirement home, where he and Riley connect over "The Price is Right." Meanwhile, Thornton goes to tell the dead agent's family about her death and Mac and Jack discuss how Mac's secretly still searching for Nikki.
#5 "Toothpick" - October 21, 2016
The Phoenix Foundation gets a tip that Nikki was spotted in Portugal, so Mac and Jack stake out the hotel she was spotted at. However, they find that the woman staying at the hotel was sent by Nikki, and gives MacGyver a key. Mac and Jack are then called by Thornton to meet Riley in Germany. The trio are called to protect a woman named Katarina Wagner (Kasha Kropinski), a secretary who discovered her boss is selling weapons to U.S. enemies. Katarina received an email from a Interpol agent Simon Abbott to take a train to Frankfurt, but the agent was killed before the email was sent. The trio are to protect Katarina on the train while Thornton confronts the CEO, Eric Wexler (Jarreth Merz). Unfortunately, she can't arrest Wexler without proof, but promises to come back.
Wexler sends a group of men to kill Katarina on the train, but they are thwarted. The men destroy the train's console, as well as the braking and coupling systems, so the train will crash into the station. Mac, using a flare, rust, and magnesium from armrests, separates the head of the train from the passenger cars, saving everyone. Katarina thanks MacGyver, asking him to call her if he's ever in Germany, and Thornton arrests Wexler. Back at home, Bozer tries flirting with Riley in order to get more digits of Riley's phone number. MacGyver goes to Nikki's apartment to try the key, but it doesn't fit anywhere. He decides to wear it as a necklace, until she is captured.
#6 "Wrench" - October 28, 2016
Mac's internal demons get externalized when The Ghost (Niko Nicotera), an old adversary whose bombs five years prior killed Mac's old C.O., Alfred Pena (Lobo Sebastian), who was supposed to be on leave to see the birth of his daughter, resurfaces. When Jack finds himself in a similar predicament that Pena was in, Mac must overcome his haunted past to defeat his rival and save Jack.
#7 "Can Opener" - November 4, 2016
The leader of a Mexican drug cartel, Joaquin "El Noche" Sancola (Raoul Trujillo), is kept in a prison in Texas. However, as a result, other members of the cartel have taken over, and cause violence in public. Mac is sent to the prison as a convict, and must break El Noche out, in order to find El Noche's cartel hideout. However, he must do it with little help, as Jack has been assigned as a guard in another part of the prison, and Riley can't hack the prison doors.
#8 "Corkscrew" - November 11, 2016
When Nikki sends an assassin to take out Mac and the rest of the team, Bozer learns who Mac and the others really are. Mac must outlast the crafty killer in a game of cat and mouse in a junkyard to save the others. When the killer is apprehended, he identifies himself as Murdoc (David Dastmalchian). Nikki meets Mac at a diner and warns him that more killers will come and to get ready to use the Portugal key. Mac returns the favor by threatening to go after her family, demonstrating how Nikki's actions have permanently changed him.
#9 "Chisel" - November 18, 2016
Mac and the team head to Latvia to capture Janis Lapa (Tobias Jelinek), a member of a terrorist organization. However, Janis sends an S.O.S out to other members, who chase Mac, Janis and the team to Latvia's US Embassy. The team must protect the embassy from the terrorists for 6 hours. Meanwhile, Bozer, while still upset at MacGyver, is held at the Phoenix Foundation to be assessed by Thornton. After learning about Bozer's prosthetic-making abilities, Thornton allows Mac to give Bozer a job at the Phoenix Foundation, which Bozer accepts.
#10 "Pliers" - December 9, 2016
The team visit MacGyver and Bozer's hometown. They go to MacGyver's old middle school, Mission City Junior High, so MacGyver can give a talk to a class taught by his former science teacher, Arthur Ericson (John Heard). They meet a young genius prodigy named Valerie Lawson (Amiah Miller), who has much in common with MacGyver, and who MacGyver and the team later need to rescue after she is kidnapped.
#11 "Scissors" - December 16, 2016
Christmas is in danger when the NSA is hacked and Riley is the main suspect. After finding out that she did to save her kidnapped mother Diane (Michael Michele), she confesses to stealing a cyber weapon, able to remotely control vehicles. Riley, MacGyver and Jack head to Shanghai before the weapon can be used and result in World War III. It is later revealed why Riley was sent to prison, as well as the reason of her animosity toward Jack.
#12 "Screwdriver" - January 6, 2017
Sarah Adler returns and has found Nikki, enlisting the team to help bring her in. However Nikki claims she is actually working for the CIA in an effort to bring down the Organization. Mac, Jack, Sarah and Nikki attempt to set up a sting to draw out a mole working for the Organization, while Riley and Bozer visit Murdoc for more information. The team later discovers that the mole is within the Phoenix Foundation.
#13 "Large Blade" - TBA, 2017
When the chopper carrying Mac & Jack is shot down in Kazakhstan, injuring the pilot and allowing a war criminal to escape, Mac must recapture him before he calls in reinforcements. Also, the team meets Matilda "Matty" Webber (Meredith Eaton), the new director of Phoenix Foundation, who happens to be Jack's ex-boss.
#14 "Fish Scaler" - February 3, 2017
Mac & Jack track down an FBI fugitive, who claims that he was forced to work for a dirty agent. The two must protect the fugitive while the team figures out who is the dirty FBI agent. Meanwhile, Bozer and Riley must meet with Matty for their first evaluation.
#15 "Magnifying Glass" - February 10, 2017
When Matty's goddaughter and her boyfriend are killed in a San Francisco park, Mac and the team investigate the crime and start to suspect that the 1970s Zodiac Killer has returned. The killer is later revealed to be working under the tutelage of a Dr. Madison Gray, who has been communicating with him from Oahu. Jack proceeds to give an old buddy of his who works on some task force in Hawaii a call about their findings.
#16 "Hook" - February 17, 2017
Mac & Jack track a dangerous fugitive down whose gets kidnapped by a notorious family of bounty hunters called; "The Coltons", (Sheryl Lee Ralph, Javicia Leslie, Lance Gross, & Jermaine Rivers). After the Coltons get the upper hand on Mac and Jack several times, a Foundation team retrieves the fugitive from them, while Mac, Jack, Bozer & Riley end up saving the Coltons' lives from their criminal employers. Meanwhile, Bozer & Riley unsuccessfully try to hack Jack's CIA file about his history with Matty.
#17 "Ruler" - February 24, 2017
The team travels to the Netherlands and during the mission become disavowed by Phoenix Foundation after the fallout from a mission designed to entrap them to fail - a contingency being activated by Patricia Thornton under her codename: Chrysalis.
#18 "Flashlight" (Crossover) - March 10, 2017
In a Hawaii Five-0 cross-over, the team reroute to Hilo, Hawaii as volunteers for Earthquake Relief with FEMA. Jack & MacGyver meet Kono & Chin from the Five-0 Task Force; Jack tells them about knowing Steve McGarrett. They rescue a group of government scientists trapped in a building by using a water jet cutter and radar detector. A Chinese group use the chaos as a distraction, aiming to steal the top-secret weaponry, called "Project 23", from the scientists in the building.
#19 "Compass" - March 31, 2017
Mac and Jack help Mac's close friend from M.I.T. Frankie (Aly Michalka) after she fakes her own death to prevent someone from killing her in order to suppress her scientific research.
#20 "Hole Puncher" - April 7, 2017
When the team intercepts a terror group's message meant for Murdoc, Mac poses as the psychopath to save the intended target and find out why they want Murdoc to assassinate him. The team realizes that the message was a trap from the Organization that Murdoc worked for, and wanted to take out MacGyver. MacGyver survives, and a member of the Organization, Daniel Holt is caught. However, while Matty is interviewing Daniel, he claims that he wanted to be caught.
#21 "Cigar Cutter" - April 14, 2017
Macgyver receives the letter he sent to his father in "Awl", as his father's whereabouts are unknown. Jack tries to distract Mac to celebrate their 3-year anniversary of surviving a mission in Cairo. Their day off is interrupted by Murdoc, who has hired a killer. The killer infiltrates the Phoenix Foundation as a Lab Technician named Dr. Zito, and wounds Bozer. Zito releases Daniel Holt, and the two take control of the Phoenix Foundation. The team work to take out Zito and Holt and restore power, while also preventing The Organization from stealing the bio-weapon from "The Rising." After stopping Zito, Holt, and The Organization, MacGyver decides to dispose of the bio-weapon in Siberia. Mac and Jack then decide to go on a road trip to find Mac's father.
On March 23, 2017, CBS renewed the series for a second season!