In Los Angeles, a black-clad man breaks into a woman's apartment. As she packs, she hears a noise in the other room. She goes to investigate and the man stabs her in the stomach and leaves. The woman's sister, Terry, comes in and sees the woman, Lila, dying on the floor. Lila warns the man who killed her is crazy before dying in Terry's arms.
MacGyver is working in a watch shop as Pete Thornton observes from a nearby surveillance watch. The storeowner is in custody and refuses to say anything. MacGyver is there to make contact with the owner's customer, Piedra, who is there to pick up a timing device for an explosive. MacGyver finds a hidden compartment with the custom-made timing devices and Thornton warns him that Piedra has carried out fourteen assassinations using different disguises and different tools. They know he's picking up the timing devices for a major hit. Thornton's man Connors spots a father and his boy entering the shop but know Piedra doesn't have a family. Inside the shop, the father lets his son pick out any watch he wants.
Terry goes to the woman who runs the escort service, Cheri, and pays an entrance fee to meet with the last "gentleman" who met with Lila. Cheri puts Lila in contact with the customer, who went under the name C.W. Smith.
The son picks out a watch and the father pays for it and then tells the boy to leave: Pete spots him leaving and figures something is up. The "father" then introduces himself as Piedra and they go in the back workshop. Piedra details what he needs and Pete hears him over the mike. As they move in, Piedra goes out front while MacGyver adjusts the device. Piedra prepares to garrote him with a watch, but MacGyver spots his reflection in the front of a grandfather clock. Piedra attacks him and MacGyver manages to break his hold and slam into a display case. Piedra throws a knife at him which MacGyver manages to block with a wooden mallet. Piedra knocks MacGyver back and comes after him with an extendible baton and then a pair of butterfly knives, but Pete arrives in time to subdue the assassin.
Cheri gives Terry the number to contact Mr. Smith, who will put her in contact with Lila's client, and tells her to make the client happy. Terry promises she will.
Pete and his men search Piedra's hotel room and check him for weapons. He has dozens of weapons on him, including a dart shooter that was used to assassinate a Central American minister.
Terry makes herself up in preparation for her date. Once she's done, she loads a revolver and puts it in her purse.
MacGyver finds exploding toothpaste among Piedra's belongings, then notices that Piedra's watch is set at 1:22 a.m. Opening it up, MacGyver finds a small packet of plastique. The phone rings and MacGyver discovers it's from a hidden scrambler case hidden beneath the desk. MacGyver takes the call: it's Mr. Smith, who asks for the time. MacGyver gives him the time from the mis-set watch: the countersign. Mr. Smith tells him he can pick up the payment at a cemetery and then tells MacGyver that the woman Piedra requested will call at 2 o'clock. Pete reveals that Piedra uses call girls to make his pickups, and then kills them. MacGyver suggests he go as Piedra but Pete is reluctant to put him in danger.
Mr. Smith goes to the cemetery with the payoff, unaware that a man is watching him. Once Smith leaves, his shadow follows with an associate. At the hotel, Pete paces nervously and the woman, Terry, makes the call at 2 p.m. MacGyver gives her instructions to pick up the briefcase with the money at the cemetery. Smith leaves the money there and leaves, while MacGyver buys flowers and meets Terry. They take his car and she drives.
Pete's men take Piedra to a safehouse, handcuff him, and lock him in a secure room. One of men brings him food and leaves.
Terry delivers the flowers to the grave and picks up Smith's briefcase, while MacGyver watches from a distance. The men who followed Smith are also there and see her make the pickup. They know about Piedra's use of call girls and figure she can lead them to the assassin. MacGyver spots them approaching and picks up Terry before they can close in. He drives off and the men follow. MacGyver pulls up to the tire barrier at a parking lot and places a board to let them get over it, then tosses it away, gets in, and has Terry drive away. Their pursuers blow out their tires trying to follow. However, when MacGyver got out Terry dropped the hotel keys and the men pick them up.
At Piedra's hotel room, MacGyver carefully opens up the briefcase and finds the money and a newspaper article on Archbishop Fierro, a Central American churchman addressing a missionary group at a convent in Los Angeles at 4 that afternoon. He calls Pete's man Connors with the information and lets them know he's on the way in, and has him check the plates of the men following him. As he hangs up, Terry draws her gun and prepares to shoot him. MacGyver picks up Piedra's rigged toothpaste and casually toys with it as Terry accuses him of killing her sister. He denies killing Lila but tosses some of the toothpaste at Terry. It explodes, distracting her so MacGyver can disarm her. He explains that he isn't Piedra and Terry explains that Lila was her only family. She breaks into tears and MacGyver promises that Piedra is in custody. He's convinced that the Archbishop is now safe and promises to be there for her.
At the safehouse, Piedra removes his fake mustache, revealing two small metal wires beneath. He twists them together and picks the lock on the handcuffs, freeing himself. He then removes a fake scar, revealing a curare-tipped wire. He takes a pea from the meal tray and sticks the wire into it, then rips apart the paper cup to make a crude blowgun. He bangs on the door and when Connors comes to investigate, blows the dart into his shoulder. Piedra grabs Connor and takes the keys and his gun and gets out, then disposes of the other four agents.
MacGyver and Terry leave the hotel but the men from the cemetery capture both of them and force them into a car. They take the briefcase and drive away, going to a church. MacGyver realizes that they’re the Archbishop's security team. MacGyver tries to explain but their leader, Emilio, notes they saw him at the cemetery and he has the payoff money. Emilio demands to know whom else is involved and MacGyver tells him that they've captured Piedra.
At the convent, Piedra has disguised himself as a limping silver-haired Irishman with a walker and learns where the Archbishop is addressing the reception. Outside, the Archbishop arrives and ignores his security team's advice to avoid the public limelight. He goes into the convent while Piedra watches him.
Emilio refuses to call Pete and MacGyver notices a nearby phone. He offers it to Terry to make the call but when Emilio tells him to put it down. MacGyver sets it on a ruler and then hits the ruler, catapulting the phone into Emilio and letting MacGyver take his gun. MacGyver then makes the call. Pete tells him that Piedra has escaped and is heading for the convent. MacGyver tells Pete to head over and has Terry explain while he and Emilio go to find the archbishop. Terry takes Emilio's gun.
MacGyver and Emilio try to convince the Archbishop to go into hiding but he refuses to give in to terror. MacGyver figures that Piedra is in disguise and they should look for someone who doesn't look like an assassin. Emilio and his men circulate through the crowd while the head nun gives an introductory speech and informs them that the Archbishop will be there after finishing a blessing service. One of the bodyguards, Lopez, spots Piedra in his disguise and closes in. The assassin spots him and leaves and Emilo and the others find his abandoned walker. The bodyguards search the chapel but are unaware that Piedra has subdued a nun and taken her habit. Meanwhile, MacGyver approaches the Archbishop and asks if he'll listen to a prayer.
In the chapel, the nuns prepare for the blessing ceremony as the Archbishop enters. One of the nuns is Piedra in disguise. He has a poisoned needle clasped in his hands. The Archbishop approaches and Piedra looks up to discover that it's MacGyver wearing the Archbishop's robes. Piedra knocks him away and makes a run for it, knocking out three bodyguards. MacGyver runs after him as Piedra goes outside. Pete and his men arrive as Piedra uses a blowgun to shoot another needle at MacGyver. MacGyver ducks and the needle bounces off the wall and imbeds itself in the paving. Terry arrives and tries to shoot Piedra: MacGyver tells her to stop and Piedra easily disarms her. The assassin launches a series of kicks to drive MacGyver back and then tries to run. MacGyver trips him with a garden hose and Piedra lands on his own poisoned needle. The assassin realizes what's happened and tries to shoot MacGyver. Piedra arrives and distracted, Piedra dies before he can make the shot.
The Archbishop gives his speech to his contributors while a satisfied Emilio thanks MacGyver for his help. MacGyver admits to Pete and Terry that he's a little disappointed he'll never know if he could have taken the assassin.