In London, MacGyver is driving through the streets and remembering a climbing expedition where he tries to haul his friend injured Paul to safety. When the line threatens to break, MacGyver promises him that no one is going to die.
MacGyver arrives at an estate and offers the invitation to the guard. He drives in for the 40th birthday party of his friend Paul Moran. Paul greets him and asks if he likes the car, and then thanks him for the letters he sent when his wife Elizabeth died. Paul's 19-year-old daughter Elise and her friend Natalia Krim come over and Paul introduces them. Paul's brother Frederick, a wealthy industrialist, comes over and talks to MacGyver in private. He explains there's already been one attempt on his life two years ago. He calls for a toast in MacGyver's honor, and a man disguised as a waiter draws a gun and shoots Frederick in the shoulder. More men drop smoke grenades and open fire. MacGyver pulls a panicked young girl down to safety while the attackers escape by motorcycle. Natalia comes over and tells them that the men shot Paul. MacGyver runs over and hears Paul whisper the words "sample pack" before dying. A guard informs Frederick that the attackers have kidnapped Elise.
Later, family friend Tony Graves arrives while Frederick demands that Chief-Superintendent Capshaw produce results. Tony offers his condolences and spars verbally with Capshaw. The superintendent gets word that they've found a body by the river. They go to the site and Frederick identifies the body as Elise's despite the heavy battering to the face.
Later, MacGyver serves as pallbearer at Paul's funeral. Afterward, the family gathers and Frederick assures MacGyver that his secretary will handle his return arrangements. MacGyver tells him that he's staying to find the people responsible for Paul and Elise's deaths. Frederick promises to support him and offers Tony as a liaison due to his background in intelligence. He suggests that Natalia help as well but she abruptly refuses and asks MacGyver for a lift home. MacGyver drops her off at her flat and she apologizes for her reaction, but refuses to tell him why. As she goes in, MacGyver notices that the door has been forced open. He peers through the mail slot but Natalia draws a gun and kicks in the door. The flat has been turned upside down and searched. She insists that terrorists are responsible and targeted her because she has been linked with Frederic in the newspapers. MacGyver finds a poison pen and realizes she's a KGB agent. She finally admits that she was studying languages in Moscow and was recruited by the KGB, but broke ties with them years ago. Now she does some work for Frederick but mostly keeps for herself. MacGyver gives her the pen and asks if she has any contacts in London. Natalia insists she doesn't want to renew her connections but MacGyver wonders why she won't help when she claims to be a friend of the family. She finally gives in and agrees to help.
The next day, Natalia sets up a meeting with Nikolai and pays him to inform them that the group responsible is violent antiestablishment anarchists who work for anyone. Nikolai offers to get MacGyver in through their leader, Joseph. Later, MacGyver goes to a warehouse and several men show up. They tell him he'll have to prove himself while Joseph watches. They attack and MacGyver blinds and defeats one man. Joseph arrives, applauds, and tosses MacGyver a gun and tells him to finish off the man. MacGyver aims the gun and then fires above Joseph's head, saying he was looking for professionals, not suicidal punks willing to sacrifice their own men. As he starts to walk away, Joseph agrees to a private meeting and says they'll contact him with the when and where later.
Later, Joseph contacts MacGyver at his hotel and arranges a meeting. Joseph tells him that the Moran job was for big money but something has turned and three of their members have disappeared. Another member has disappeared. He tells MacGyver to meet them in the fourth quadrant of the sewers. They have a handwritten message from the person who hired them, and they want MacGyver to recover them to cover themselves. MacGyver meets with Tony and Natalia, and Tony insists that MacGyver wear a wire. Tony takes offense and Natalia gets him out, and then apologizes for the man's stubbornness. MacGyver asks her to make up a list of who might have hired Joseph… including Frederick's friends.
MacGyver goes to the flat at the address provided and finds Joseph and another terrorist, shot dead. There are maps of the London sewers with a location marked with a IV. MacGyver goes down into the sewers and finds a IV scratched into the wall beneath a pipe leading upward. As he reaches inside, a rat leaps on his hand and MacGyver jerks back, knocking the watch crystal and bezel off of his wristwatch. Inside the pipe he finds a bag containing the handwritten instructions. As he examines the note, MacGyver hears something but assumes he misheard. According to a newspaper article attached, Paul was the target. Before he can read the note, someone drops gas canisters in and MacGyver clutches at his eyes in pain. Using the note and coal dust from a bucket, he manages to protect himself long enough to get outside before collapsing facedown in a puddle of water.
The next morning, MacGyver wakes up naked in bed with Natalia. She assures him that he's all right and explains that Nikolai found him and brought him to her. She says that since he had fevers and chills, she stripped him naked and lay with him to maintain his body temperature until his fever broke. She gets up and says that they need to go to work, and then tosses him his clothing. MacGyver tells her that the people who hired the terrorists tried to kill him and that Paul was their intended target. He wants to get into Paul's lab and Natalia tells him that Tony can get them in since his company funded Paul's work.
Natalia and MacGyver go to the police station where Tony informs them that there was a break-in at Paul's lab. They go to the lab and meet with Dr. Massey, who explains that Paul was fine-tuning a portable mass spectrometer, capable of measuring the slightest nuclear presence. All the records, files, and air samples from all over England are missing. Capshaw arrives and complains about Tony being there, and orders them all out. The two argue and Capshaw points out that Tony has been arrested before on multiple assault charges. Outside, MacGyver notes that Paul mentioned samples and asks Dr. Massey if he knows anything about them. The doctor explains that Paul kept all of his work to himself, and slept in a small room upstairs. MacGyver searches it, unaware that Natalia is watching him from hiding. MacGyver finds Paul's old mountain-climbing gear and an air sample cylinder, but Capshaw comes in and orders him out. He tells MacGyver to stay out of the investigation.
Outside, MacGyver tells Natalia that he needed just two more minutes, but refuses to explain why to Natalia. He offers to take her home and she wonders why he suddenly doesn't trust her. She takes offense but MacGyver warns that he can't trust anyone. However, she notes that he needs her and shows him the cylinder that she managed to steal when no one was looking. As they drive back, Natalia explains that Tony was an American intelligence operative serving in Great Britain. A terrorist suspect died during questioning and Capshaw was present as a young officer. Tony's involvement was never proven and Capshaw believes his career was smeared as a result.
At the lab, MacGyver get an analysis performed on the contents of the cylinder and confirms that it shows high levels of U-235. It confirms that someone is operating an illegal nuclear plant in England and Paul found it. MacGyver figures that someone might be supplying terrorist countries with nuclear material for bombs. Natalia warns that they're both under suspicion and offers to find them a safe house they can use.
MacGyver goes to the library to locate where the cylinder came from, unaware that Capshaw is following him. Inside, MacGyver notices a label marked "CARE" on the cylinder and realizes that the E is actual a C. Going through the books, he finds a reference to Carcroft Castle in Sussex. The castle was last purchased in 1983 Lyndover Ltd., a trading company, and MacGyver discovers that Tony is the company director. As MacGyver gets into his car outside, he hears a ticking noise and jumps clear just as the bomb explodes, destroying the car.
As MacGyver is checked for injuries, Capshaw arrives to tell him they're going to talk about manners. The chief-superintendent insists that MacGyver turn over what he's learned but MacGyver refuses. Capshaw wonders about his association with Tony but MacGyver insists that he's not allied with anyone.
MacGyver and Natalia tell Frederick what they've discovered about Tony but the industrialist isn't convinced. However, he notes that he severed ties with Tony after the man wanted to acquire more money. MacGyver has done a background check and notes that Tony's history is cleaned. They decide to figure out how deep the conspiracy goes before going to the authorities and Frederick says he'll fully back MacGyver.
MacGyver goes to Tony's flat and breaks into his apartment through an open window. He finds Tony dead, and Capshaw bursts in and accuses him of murder. MacGyver's watch crystal is lying on the floor and Capshaw places him under arrest. MacGyver leaps out the window, injuring his shoulder, and runs into the underground subway with the police in hot pursuit. He ducks into a carriage but Capshaw and his men close in. MacGyver ducks into the driver's cabin but Capshaw realizes he's in there and orders everyone back. He opens the door only to discover that MacGyver has slipped out. He orders his men to go outside and continue the search, unaware that MacGyver has hidden behind a track mirror. Once the police are gone, MacGyver slips away.
Natalia is waiting when MacGyver arrives. He accuses her of setting him up for Tony's murder but she insists that she's innocent and Capshaw is responsible. Natalia suggests that Tony and Capshaw were partners and the hostility was just a façade. She points out that MacGyver dragged her into the investigation and says that she's on his side all the way. MacGyver says he needs time to think and Natalia tells him that Nikolai has been hired for a job based on his knowledge of nuclear facilities. She promises to find out everything Nikolai knows.
Capshaw goes to see Frederick and request any information he has on MacGyver's whereabouts. Frederick orders him out.
Natalia calls MacGyver to tell him she'll rendezvous with Nikolai, and if something happens that he should leave in one hour. As MacGyver arrives at the rendezvous site, he watches as Natalia is gunned down. The killers pursue him down the street and into the sewers. He gets to a door and finds it locked. The killers move in behind him and assume he's escaped down a side tunnel. Once they move on, MacGyver remains hiding in the pipes above until the next morning when workers arrive.
MacGyver heads to Carcroft Castle and hitches a ride with a biker, Plato. They spot a police roadblock up ahead and MacGyver asks Plato for his help. The biker goes through the roadblock while MacGyver circles around through the woods and meets him on the other side. They proceed to Carcroft and Plato drops MacGyver off. He then sneaks into the castle grounds and finds armed guards patrolling the walls. MacGyver scales a pipe and gets over the wall and into the castle. A telephone rings and MacGyver follows the sound to an office where he discovers Dr. Massey using truth serum to force Elise to give them the software code for Paul's spectrometer. Massey wants the information that her father kept to himself, and they need the information to secure the plant from further detection. MacGyver knocks him out with a book and is forced to tell Elise that her father is dead. She explains the terrorists drugged her and brought her to the castle, but she doesn't know who is responsible. The person responsible is processing nuclear material beneath the castle, and the first shipment leaves today in two tactical weapons.
MacGyver promises to come back for her and then goes to find the door leading to the basement facility. He finds the controls but before he can do anything, Frederick arrives with a gun and takes him captive. He explains he was forced to order the death of his own brother in return for enormous profits. Frederick boasts of building a state-of-the-art nuclear plant in the middle of Britain, but Paul found it. MacGyver grabs a lever for the nearby vacuum pumps and activates them, pulling Frederick back toward and knocking him out.
MacGyver goes into the plant and finds the control room, containing one of the tactical nuclear devices. Natalia reveals that she's in and blames MacGyver for succeeding so that she is the one forced to kill him. She refuses to allow the dissolution of the USSR and is going to kill MacGyver to complete her mission as a KGB agent. Frederick arrives and tells Natalia to finish MacGyver off. MacGyver points out that she doesn't care about her people and is going to kill thousands to preserve Communism, and she's working with a capitalist like Frederick. She admits that MacGyver is correct and then shoots Frederick.
MacGyver runs out and jams the door and then uses an oscilloscope to project a high-pitched noise to deafen Natalia. He turns off the temperature controller and hides. Natalia arrives and undoes his sabotage, while MacGyver strips off some insulation and climbs the heated pipes above. He climbs down and goes back to the control room and then overrides the pump controls to destroy the U-235. The automatic override engages and MacGyver shuts that down as well, and then shoves Natalia away when she tries to interfere. She grabs a knife and throws it into MacGyver's leg, and then takes the manufactured U-235 and places it in the tactical device, arming the bomb. She warns that it can't be disarmed without a trigger wrench, and they have just over a minute left. He punches her unconscious and then uses a tennis racket and three clips to get the bomb open and disarm it with two seconds to spare. Natalia wakes up and MacGyver tells her it wasn't meant to be.
Later, Capshaw offers an apology to MacGyver and thanks him for his help. After he leaves, MacGyver tells Elise that with Paul gone, it's up to them to help the planet.