A black-clad man breaks into a Los Angeles apartment and stabs a call girl in the stomach, then leaves. Her sister, Terry, comes in and finds Lila dying on the floor. Terry asks Lila who killed her but Lila can only warn that her killer is crazy before dying in her sister's arms.
MacGyver is pretending to be a watch shop owner as Pete Thornton and his lieutenant, Connors, watch from a surveillance fan. MacGyver has replaced the owner, who is under arrest because he's connected to Piedra, a top assassin responsible for 14 assassinations who plans to buy an explosive timing device for an upcoming mission. Searching the shop, MacGyver finds a hidden compartment with the timing device. Connors spots a father bringing his son into the shop but Pete assures him that Piedra has no known family.
Terry visits Cheri, the woman who runs the escort service that Lila worked for. Terry pays an entrance fee to meet with the same client that Lila met with. Cheri promises to put Terry in contact with Mr. Smith, the man who represents Lila's last client.
The boy, Eddie, picks out a watch and his "father" pays for it and sends him on the way. He introduces himself as Piedra and asks for the timing device. Pete and Connors spot Eddie emerging alone and figure something is up. They hear Piedra talking to MacGyver over the hidden two-way transmitter, describing what he needs. MacGyver assures him he has the device and needs to make a few adjustments. Piedra steps out but then pulls a hidden garrote from his wristwatch. MacGyver spots Piedra's reflection in a grandfather clock but Piedra attacks him and MacGyver throws him into a display case. Undeterred, Piedra throws a knife which MacGyver catches on a mallet. Piedra throws a kick at MacGyver and the two spar, Piedra producing an extendible club and a pair of knives. Piedra finally corners MacGyver… and Pete knocks him out from behind. MacGyver claims he had the killer right where he wanted him.
Cheri gives Terry Smith's number and tells her that her job is to make the client happy. Terry assures Cheri that she will. Afterward, she prepares for her meeting and loads a gun.
Pete's men search Piedra and produce dozens of weapons, including a dart tipped with curare that was used in the assassination of a Central American minister. MacGyver also finds a tube of fake toothpaste that explodes on impact. Finally he discovers that Piedra's watch is set to the wrong time. It also contains a small packet of plastique, enough to blast a cell door open. The phone rings but it's not the hotel room: it's a hidden phone with a state-of-the-art scrambling unit. MacGyver answers the phone: Smith is on the other end and asks for the time. MacGyver gives him the time no Piedra's watch and Smith tells him that he can pick up his payment and orders at a cemetery by a particular grave. Smith informs MacGyver that the woman he requested will meet with him at 2 o'clock. After he hangs up, Pete warns that Piedra uses call girls to pick up his payment and then disposes of them once and for all. MacGyver says that he'll go in pretending to be Piedra. Pete reluctantly agrees as MacGyver is the best man for the job.
Smith drives to the cemetery, unaware that two Hispanic men are following him. Meanwhile, Terry calls Piedra's hotel room and MacGyver takes the call. He tells her to meet him at a specific location. MacGyver buys flowers and meets her, and he has her drive to the cemetery. Smith has left the money there and the men following him have stayed there to see who picks it up.
Connors and four other DXS men take Piedra to a safehouse, handcuff him, and lock him in a cell. They leave him a tray of food with no metal utensils and leave him alone.
Terry takes flowers to the grave and gets the briefcase with the money. The men who followed Smith go after her, knowing that Piedra uses call girls to pick up his money. MacGyver spots them and gets Terry and then drives away. The men follow and MacGyver pulls up to a parking lot tire barrier and uses a board to drive over it while Terry takes the wheel. Once they get over the barrier, MacGyver tosses the board away and they escape while their pursuers blow out their tires. However, the lead pursuer, Emilio, finds the hotel key that Terry dropped when she switched seats.
MacGyver takes Terry to the hotel room and finds Piedra's payoff and a newspaper article on Archbishop Fierro, a Central American churchman in Los Angeles to give a speech to his contributors at a convent at 4 p.m. MacGyver calls Connors and lets him know what he's found out, and tells him to check out the license plate of the men following them. MacGyver looks up to find Terry ready to shoot him in revenge for Lila. He tries to explain that he isn't Piedra while toying with Piedra's fake toothpaste. He smears some on his fingers and shakes it off, and the mini-explosion startles Terry, letting him disarm her. When he points out that she'd be dead if he was Piedra, she collapse sobbing in his arms. MacGyver reassures her that they have Piedra in custody and the archbishop is safe.
At the safehouse, Piedra removes a fake mustache. Two piece of wire are hidden beneath and he twisted them into a lockpick. Once he opens the handcuffs, he removes a fake scar hiding a piece of wire tipped with curare. Piedra then makes a crude blowgun out of a paper cup and uses a pea as a counterweight on the wire. He bangs on the door and when Connors orders him back, Piedra shoots the dart into Connors' shoulder. The killer then grabs the paralyzed man and takes his keys and his gun. Going out, Piedra disposes of the other four DXS agents in short order.
As MacGyver and Terry leave the hotel, Emilio and his men force them into a car at gunpoint. They drive to the basement of a church and MacGyver realizes the men are the Archbishop's bodyguards. He tries to explain he isn't Piedra but Emilio points out that he has the briefcase with the money. MacGyver tries to explain what happened but Emilio doesn't believe him.
Piedra prepares to carry out his mission, disguising himself as an elderly Irishman with a walker. He arrives at the convent and works his way through the crowds. Outside, the Archbishop arrives and informs his bodyguards that he has to give his speech thanking the contributors to the cause. Piedra watches as the Archbishop goes into the convent to prepare for his speech.
MacGyver tries to convince Emilio to call DXS and confirm his story. When Emilio refuses, MacGyver picks up the phone and sets it on a ruler lying on the desk. He then levels the phone up into Emilio's face and disarms him when he's distracted. Once he has the gun, MacGyver makes the call and learns that Piedra has escaped. Pete heads for the convent and MacGyver puts Terry on the phone to explain. As he and Emilio go to warn the Archbishop, Terry picks up Emilio's gun.
The two men try to convince the Archbishop to postpone his speech but the churchman is adamant that he carry out God's will no matter what threat is made against his life. MacGyver and Emilio search the crowd, figuring that Piedra is disguised as the least likely person to be a killer. As the Archbishop prepares for a blessing ceremony in the chapel before giving his speech, one of the bodyguards spots Piedra and moves in. Piedra escapes through the crowd and into the convent. Once inside, he subdues a nun and drags her into a nearby room. MacGyver goes to see the Archbishop and asks if the churchman will hear a prayer.
The nuns go to the chapel for the blessing ceremony and a man wearing the Archbishop's robes enters. One of the nuns is Piedra in disguise, holding a poison needle. He looks up when the Archbishop steps in front of him: it's MacGyver. Piedra slams him back and runs out of the chapel, knocking out every bodyguard in his way. MacGyver recovers and follows him outside. Piedra spins and fires a needle from a blowgun. MacGyver ducks and the needle bounces off the window and embeds itself in the sidewalk mortar. Terry approaches Piedra and prepares to shoot him, but he takes the gun and then attacks MacGyver. Once MacGyver goes down, Piedra runs past him but MacGyver trips him with a garden hose and the assassin breaks his fall... but his hand lands on the needle. He staggers to his feet and tries to shoot MacGyver, but Pete arrives and distracts him long enough for the poison to take full effect.
Later, the Archbishop gives his speech while MacGyver, Pete, and Terry look on. Emilio thanks MacGyver for his help and MacGyver admits that he's disappointed he never found out if he could take Piedra.