MacGyver arrives in London to attend the 40th birthday celebration of his friend Paul Moran. As he drives out to Paul's estate, MacGyver remembers how he saved Paul's life, hauling him to safety during a mountain-climbing expedition. He arrives and security passes him on. MacGyver meets with Paul, who asks him how he likes the car he loaned him. Paul thanks him for sending him a letter expressing his condolences upon the death of his wife Elizabeth, and MacGyver admits that he wishes he could have been there but he was on assignment.
Paul introduces Elise, his 19-year-old daughter, and her friend Natalia Krim. Paul's brother Frederick, a wealthy industrialist, comes over and asks to talk to MacGyver in private. Frederick explains that the increased security is due to the threat of assassination. Frederick then asks everyone to gather round and offers a toast to MacGyver for saving Paul's life on the mountain. Men disguised as waiters open fire, shooting Frederick in the shoulder and dropping smoke bombs. They escape by motorcycle and Natalia tells MacGyver that they shot Paul. MacGyver runs to his dying friend, who whispers "sample pack" to him before dying. One of the guards informs the wounded Frederick that the intruders abducted Elise.
Later, the police arrive and Chief Superintendent Capshaw tries to investigate the attack. The Morans' family friend, Tony Graves, arrives and offers his condolences. He and Capshaw know and dislike each other from some past encounter. Capshaw gets word that his men have found a young woman's body at the river. They go there and discover that the corpse's face has been badly beaten. Nonetheless, Frederick identifies it as Elise.
After Paul's funeral, the family gathers and MacGyver informs Frederick that he'll be staying to track down the men who killed Paul and Elise. Frederick suggests that Tony act as a liaison, since he has worked in intelligence. Natalia is there and Frederick asks that she help. She refuses and asks MacGyver for a lift home. As he drops her off, Natalia apologizes for her refusal but doesn't wish to tell him why. As she approaches the door, MacGyver notices that the lock has been broken open. Natalia kicks the door down and draws a gun. Someone has thoroughly searched the place and Natalia believes the terrorists from the party are responsible. She insists that they read the newspaper articles that linked her to the Moran family. However, MacGyver finds a pen with a poison cartridge and recognizes it as KGB equipment. When he confronts Natalia, she admits that she was recruited by the KGB years ago, but broke off her ties with the organization after the fall of the Soviet Union. Now she occasionally works for Frederick but tries to live a quiet life and forget her past. MacGyver asks her to check her former KGB connections in London and see what she can find out about Paul and Elise's death. Natalia insists she doesn't want to help but MacGyver points out she owes it to the Morans and the woman reluctantly agrees.
Natalia sets up a meeting with Nikolai. The man confirms that the terrorist group are violent antiestablishment anarchists who work for the highest bidder. Nikolai sets MacGyver up as a potential recruit and gives him an address where he can find the group's leader, Joseph. MacGyver goes to the specified address and find several of the anarchists waiting for him. Joseph watches from above as the men attack him and demand that MacGyver prove himself. He manages to blind one man and take him down. Joseph gives MacGyver a gun and tells him to finish the downed anarchist. MacGyver fires the gun above Joseph's head and insists that he's not interested in petty games, and that he's there to work with professionals. MacGyver feigns disgust and starts to leave, and Joseph agrees to take him on. He tells MacGyver that they'll contact him when they're ready to hire him.
Later, MacGyver receives word that Joseph wants to see him. He meets and Joseph explains that someone anonymously hired his group to attack the birthday party. Since then, four of the group's members have disappeared. He wants MacGyver to recover the handwritten message from their employer and explains it's hidden in the fourth quadrant of the sewers. MacGyver aggress and Joseph tells him to meet later at his flat. MacGyver then meets with Natalia and Tony. Tony suggests he takes a wire and is offended when MacGyver refuses, insisting it would incriminate him if it were discovered. Natalia hastily ushers Tony out and apologizes for his behavior. As he goes, MacGyver asks her to make up a list of anyone who would have hired Joseph's group... including Frederick's friends.
MacGyver gets word where to meet Joseph and goes to the man's flat. He finds the leader dead, shot. MacGyver searches the place and finds a map of the London sewer with the fourth quadrant marked. MacGyver goes there and looks for the employer's note. As he searches, a rat jumps on his hand and he jerks it back, knocking the bezel off of his wristwatch. He finally finds the note stored in a bag. A newspaper article attached to it confirms that Paul was the target. Before MacGyver can more than glimpse the handwriting, someone drops gas canisters into the sewer. MacGyver makes a gas filter out of the note and coal dust, but he still receives a heavy dose of poison and collapses before he can get far.
MacGyver wakes up the next morning to find himself naked in bed with Natalia. She tells him that Nikolai found MacGyver and brought him to her. Natalia stripped him naked and then got in bed with him to stabilize his body temperature until his fever broke. She gets out of bed and tosses him his clothes, and then tells him they have work to do. MacGyver tells her what he's discovered and says that they should go to Paul's lab. Natalia agrees and informs him that Tony owns the company that funded Paul's research, and that he can get them in.
When they contact Tony, he asks them to go to the police station. He tells them that there was a break-in at Paul's lab. They arrive there and Dr. Massey's, Paul's co-worker, explains that Paul was working on a portable mass spectrometer calibrated to measure nuclear fuel. The thieves stole all of the research and samples that Paul had gathered. When Capshaw arrives, he takes offense at Tony's presence and orders them all out. Tony argues over the inspector's decision and Capshaw notes that Tony has been arrested before for assault. As they leave, MacGyver asks Dr. Massey if he knows about the sample pack that Paul mentioned. Dr. Massey informs him that Paul kept his findings to himself and lived onsite in a small upstairs apartment. MacGyver searches the room, unaware that Natalia is secretly watching him from the door. He finds an air sample cylinder and Paul's old mountain-climbing equipment. Before he can look further, Capshaw arrives and tells him to stay out of the investigation.
As he leaves, MacGyver explains to Natalia that he was close to finding what he needs, but refuses to go into specifics. When he offers to take her home, she asks why he doesn't trust her any more. MacGyver admits that he can't trust anyone, but she tells him that she managed to steal the air sample cylinder, so he doesn't have a choice. As they drive back, MacGyver wonders why things are tense between Tony and the inspector. Natalia explains that Tony was an American intelligence operative working in England. When a terrorist died during questioning, Tony and Capshaw were present. Capshaw blamed Tony and believed the death caused his superiors to put a black mark on his own record.
They return to the lab and analyze the samples. The tests confirm that the samples contain high levels of U-235, showing that someone is operating an illegal nuclear plant to create nuclear material for bombs. MacGyver concludes that Paul found out and the anarchists' employer needed him dead before he could reveal what he knew. Natalia offers them a safe house to use since Capshaw suspects both of them.
MacGyver goes to the library to try and identify the word CARE on the cylinder, unaware that Capshaw has him under surveillance. As MacGyver examines the cylinder, he realizes that the middle line in the E is a scratch, and the location ID is actually CARC. He determines that there is a Carcroft Castle in Sussex, and it was purchased by a company owned by Tony. MacGyver goes to his car but hears a ticking noise. He jumps away just in time as a bomb explodes, destroying the car.
Capshaw calls in the medics to have MacGyver examines, and demands that MacGyver turn over everything he's found out. MacGyver refuses and Capshaw questions his association with Tony. In response, MacGyver insists that he isn't working with anyone, but simply trying to get at the truth.
Capshaw has no choice but to release MacGyver, and he and Natalia go to see Frederick. They tell him what they've discovered but Frederick refuses to accept that Tony is a killer. However, he admits that Tony did want to acquire more money through some scheme and Frederick severed his business ties with him. They check Tony's record and discover that his background is a blank, suggesting some influential person covered Tony's tracks, possibly someone in the government. They realize that they can't trust anyone in authority and will have to investigate further on their own.
MacGyver goes to see Tony at his flat and finds the man dead. Capshaw and his officers burst in and accuse MacGyver of the murder. MacGyver denies it but Capshaw points out that his wristwatch bezel is lying next to the corpse. When Capshaw tries to arrest him, MacGyver jumps out the window, twisting his shoulder. He runs into the underground and enters one of the carriages. When the police pursue, MacGyver slips out through the driver's cabin and hides behind the track mirror until Capshaw and his men leave.
MacGyver returns to the safe house and accuses Natalia of setting him up. She denies it and insists that Capshaw set the whole thing up. She speculates that Capshaw and Tony were partners and Capshaw finally decided to eliminate his ally and pin it on MacGyver. Natalia argues that MacGyver is the one who forced her to help, and she's supported him the entire time, saving his life from the poison gas. MacGyver considers what she's said and Natalia tells him that Nikolai has told her that he's been hired for a job involving nuclear facilities. She says she'll meet with the man and find out what he knows.
Unable to find MacGyver, Capshaw goes to see Frederick and warns that he's interfering in an investigation. Unimpressed, Frederick orders him out.
Natalia calls MacGyver and tells him that she's set up a meeting with Nikolai. MacGyver goes there and arrives just in time to see someone gun Natalia down. The killers come after him and he slips into the sewers. MacGyver manages to lose them in the sewers and is trapped until the next morning when workers arrive and are surprised to find him there.
With no other leads to follow in London, MacGyver makes his way to Carcroft Castle. He hitches a ride with a biker, Plato, and asks the man to help him get past the police roadblocks. Plato distracts the officers at one roadblock while MacGyver slips around through the woods and meets him on the other side. Plato takes him the rest of the way to Carcroft and wishes him well.
MacGyver slips past the armed guards and gets over the castle wall, and enters the castle. He hears a phone ringing and follows the sound to an office where Dr. Massey is interrogating... Elise, who is alive. Massey is using sodium pentothal to force her to reveal her father's software codes so he can access the spectrometer and prevent anyone else from finding the hidden nuclear facility. MacGyver knocks Massey out with a book and admits to Elise that Paul is dead. She tells her that the anarchists kidnapped her, faked her death, and brought her to the castle. However, she doesn't know who hired them. She warns that the person in charge is processing nuclear material and that he has enough for two tactical weapons, which will ship that day.
MacGyver has her stay in the room and then slips down to the basement where the entrance to the nuclear plant is. Before he can enter, Frederick arrives and holds him at gunpoint. He tells MacGyver that he was forced to have Paul killed to protect his new financial empire. Frederick secretly built the plant but Paul discovered it using his spectrometer. MacGyver notices the release pipe for a vacuum pump. He grabs the lever and activates it, pulling Frederick back and knocking him unconscious.
Entering the plant, MacGyver finds the primary control room and the tactical weapon. As he examines it, Natalia steps out and reveals that she's still working for the KGB. They plan to use the nuclear weapons to force the Soviet states to reunite, and she has no choice but to kill MacGyver before he can thwart their scheme. Frederick arrives and tells her to kill MacGyver, and MacGyver points out the irony of her taking orders from a capitalist. Natalia concedes the point and shoots Frederick.
As she shoots, MacGyver runs out and jams the door. He uses an oscilloscope to create feedback to deafen Natalia, and then turns off the reactors temperature controller. While Natalia reverses the sabotage, MacGyver strips off piping insulation and uses it to make knee and hand pads so he can cross the heated pipes above her and get back to the control room. He overrides the pump controls and the control overrides to destroy the U-235. Natalia returns to the control room and throws a knife into MacGyver. She shoves him aside and takes the U-235, and places it into one of the tactical weapons. As she arms the bomb, she informs MacGyver that it can't be disarmed without the proper trigger wrench.
With less than a minute left before the bomb goes off, MacGyver overcomes his injury and knocks her unconscious. Spotting a nearby tennis racket, he attaches three clips to the racket's wiring so that he can untwist all three screws on the bomb simultaneously. Once the bomb is open, MacGyver manages to stop the countdown with two seconds to spare. Natalia wakes up and MacGyver tells her that she's failed.
Later, Capshaw shuts down the plant and apologizes to MacGyver. As MacGyver and Elise leave, MacGyver tells her that with her father dead, they all have to do their part to help the planet.