On Halloween, MacGyver arrives at the courthouse to testify against Dr. Zito. Lt. Murphy and Pete are there to provide support and watch the case. They note that Zito has been acting the perfect gentleman so far, and that Dr. Marion Skinner is testifying that he's cured.
MacGyver takes the stand and describes how he met Zito two years ago when working the Eric Cross case. He explains how Zito engineered fellow inmate Cross' escape and psychologically manipulated him into trying to kill Murphy, the officer who arrested Zito. MacGyver describes Zito as "evil," soliciting an objection from Skinner. Unfortunately, there is no evidence to prove Zito's involvement with Cross, and Cross committed suicide shortly after he was recaptured. Nevertheless, the judge rules that Zito is far too dangerous to be released and orders him back to the state mental hospital.
After the trial, Zito thanks Skinner for her help and borrows a pen to sign an appeal. His orderly makes sure he returns the pen, and Zito apologizes for his absent-mindedness. As he's taken out, Zito chats with MacGyver and Murphy and notes how it's ironic that the fates have brought them together. He admits he's surprised that MacGyver labeled him evil, and promises to give him a lesson in what evil really is.
Outside in the hallway, Zito asks to use the drinking fountain. As he bends down, he slips out the ink refill cartridge he secretly took from Skinner's pen. The two orderlies take him on the elevator and it starts to descend. Meanwhile, Skinner insists on defending Zito, claiming he's cured. They're interrupted by screams: a legal secretary has found the orderlies' corpses in the elevator. While the security guards check the bodies, Zito climbs down the elevator shaft, steals a bailiff's uniform, and casually strolls out of the courthouse. A nauseous Skinner goes outside to get some fresh air and sees Zito give two trick-or-treaters the bloody ink cartridge. However, by the time she summons the police, he's long gone.
Captain Michael Kiley conducts the investigation and finds a note addressed to MacGyver. It says that his lesson in evil has begun, and has a mathematical formula. The answer is 4, and MacGyver concludes it refers to Zito's cell number. He and Murphy go there and finds a deck of playing cards on the table. Inside they find Zito's library card. As they leave, Zito calls and tells MacGyver he'll find the next clue outside the hospital by the payphone. They run outside but Zito has already left. A nearby shopping cart holds a roll of twine, a set of scales, and a pair of garden shears. Another formula is written on the phone booth glass, yielding an answer of 15.
MacGyver and Murphy go to the police station with every book that Zito checked out from the mental hospital. With Skinner's help, they go through the books looking for any connection to the number 15. Finally they find a book on Greek mythology and page 15 discusses the three Fates of ancient Greece. There's also another formula, yielding the number 3. MacGyver recalls Zito talking about fate at the courthouse. Zito calls again and talks about how evil is unpredictable and can strike at friends, families, and co-workers, then hangs up before they can trace the call.
At the Phoenix analysis lab, Pete finds another formula written in fluorescent on the handle of the shears, providing an answer of 20. After calling MacGyver with the information, Pete heads for the police station. Murphy is talking about dealing with Zito once and for all, and Skinner protests. While Kiley reassures Skinner that they'll follow procedure, MacGyver goes over the recording of Zito's call. They know that Zito is familiar with police procedure and used it against Murphy during the Cross case, and MacGyver realizes that Zito has anticipated Pete taking the shears to the Phoenix analysis lab. Further, the number 20 is Pete's parking slot. MacGyver tries to call Pete, who is already in his car. He turns on the headlights and sees another formula on the wall ahead, with an answer of 15. Zito is hiding in the back seat and captures Pete, then takes him to a cell and chains him to the wall. Zito muffles him with a leather gag and explains how it was used to keep patients from biting off their tongues.
MacGyver and Murphy get word of Pete's abduction and the new number. As they go through the book on Greek mythology, MacGyver notes that the Fates held string, shears, and a scale. Kiley informs them that Zito dropped off Pete's car in front of the station. Inside the trunk is MacGyver's doormat. They go to his houseboat and find Pete tied up on the floor. As MacGyver unties his friend, Murphy follows procedure and conducts a room-to-room search. Pete and MacGyver spot another formula painted on the wall, and a P.S.: "Goodbye, Murphy." A booby trap goes off, slamming Murphy into the floor.
As the EMTs tend to the badly injured Murphy, Kiley and Skinner arrive. Skinner apologizes to Murphy, and the lieutenant admits that she was too emotional and Zito knew she'd follow procedure. Pete is unable to remember anything useful about where he was kept other then that it was an old building and he was gagged. Skinner remembers her sessions with Zito when the doctor said he'd like to retire to a monastery if he acquired his freedom. She goes to get her taped transcripts of her sessions with Zito. MacGyver adds the most recent answer, 18, to the other five. He realizes that 4 – 15 – 3 – 20 – 15 – 18 correspond to the letters of the alphabet, spelling out "doctor."
Outside, Skinner discovers her car doesn't work. She hails a nearby cab and discovers that her car battery is on the floor. The driver, Zito, turns around and informs her he removed it for her, then locks the doors and drives away.
Later, MacGyver goes over the transcript tapes at the station. Zito calls to tell him he has one hour to find his sanctuary and to come alone. If MacGyver doesn't arrive in time, Skinner dies. Zito has chained Skinner in a tub and hangs an electric heater on the inside edge. He then turns on the water while explaining that mental patients used to be treated by immersing them in freezing water.
Based on Pete's description of his cell and the gag Zito used on him, MacGyver realizes that Zito is hiding in an abandoned asylum that was originally a monastery. He goes there alone and enters through a window. He finds Skinner but Zito has locked her cell door and has the only key. Zito goes up into the bell tower and waits for MacGyver to arrive. He holds MacGyver at gunpoint and tells him that MacGyver must kill him to "pass" his lesson. Zito carefully sets the gun down on the floor and tries to goad MacGyver into killing him. When MacGyver balks, Zito says that he'll pay a visit to Murphy and finish the job. MacGyver starts to pick up the gun, but notices a rope beneath the walkway that leads to the monastery bell. MacGyver tells Zito he's solved his riddle. The Fates are the solution: the rope is their string; the gun is their shears. Only the scales are left, signifying a balance. MacGyver touches the section of flooring the gun is on, and which Zito has rigged to move when the gun is lifted. The bell swings into MacGyver, knocking him down. The two men struggle and Zito knocks MacGyver off the walkway. MacGyver hangs on and Zito says the game is over and steps on his fingers. MacGyver lets go and grabs the bell rope, swinging it into Zito. MacGyver climbs back up and ties Zito up with the bell rope, then takes the key and leaves Zito hanging. With seconds to spare, MacGyver unlocks the cell door and smashes the electric heater against the wall.
Later, MacGyver brings the recovering Murphy to the police station where everyone greets her with a surprise party. Skinner assures them that Zito is back in his cell and will never escape again. She's unaware that Zito has concealed a small lockpick underneath a fake scar and is preparing for another escape...