Four teenager vigilantes calling themselves the Tough Boys are cleaning out their neighborhood, blowing up drug labs using military tactics and explosives. However, when they inadvertently kill a drug dealer, one of them begins to have doubts.
R.T. Hines is starting a new self-esteem project at the Challengers Club and MacGyver goes to see if it deserves Foundation funding. He arrives and talks to his friend Manny, a policeman who retired to Nebraska with his wife but has returned to the job after she divorced him. He greets MacGyver and assures him that the Club's membership has tripled since Hines started the program. However, he warns MacGyver that Hines is a disciplinarian. Hines is running a class through military-style exercises. Among his students is Coco Hubbard, a former gang leader who left the gangs to join the program. Angel Royas, another teen, swaggers into the class, drunk. Hines confronts him and shoves his head into a bucket of soapy water. MacGyver intervenes, and Hines accuses him of being a "tourist," only passing through while Hines is working every day to stop the violence on the streets.
A drug lord, Dennis, meets with his men Harris and Myron on his yacht at the docks. He warns that the Tough Boys are getting favorable coverage because of their attacks on his distribution centers.
At the club, Coco and his friends Hector and Sinclair are watching a news broadcast on the Tough Boys and the fact someone has finally died during one of their attacks. They discuss whether Angel is with them or not but drop the subject when they notice MacGyver observing them. Later, the three boys confront Angel, who is preparing to leave town. He fights back, hitting Coco, before the others can subdue him. Angel says that they should have saved the drug dealer who died in the fire, but Coco insists that they've all lost someone to drugs. He promises that there won't be any more deaths and that "The Man" is sending them after some rich boys who are sending the drugs into the neighborhood. As they leave, Coco takes one swing at Angel for payback for the hit he scored on him and hits him in the eye.
MacGyver goes to one of the burndown sites where Manny is investigating. He tells his friend that he suspects Hines is organizing the Tough Boys but Manny insists that there are plenty of other possible candidates. He warns MacGyver that the drug lords have put a price on the Tough Boys head and that MacGyver shouldn't get caught in the crossfire.
Dennis tells his men to check out the three men that he believes are leading the Tough Boys. One of them is R.T. Hines.
When MacGyver returns to the club, he notices Angel's black eye. Hines interrupts before MacGyver can learn anything, and denies hitting Angel. MacGyver agrees with him, saying the person who hit Angel didn't use the same hand that Hines does. Hines orders him that it's dangerous and he should stay out of business that doesn't concern him. Once MacGyver has left, Coco and his friends worry that MacGyver is getting too close. Coco tells the others that The Man has passed on orders to tag MacGyver and scare him off.
As MacGyver is driving down the streets, one of the Tough Boys runs across the back of his truck and ducks into an abandoned building. MacGyver takes the bait and follows, pursuing them up the stairs. He comes to a locked cage door but instead of going around, picks the lock and enters. The Tough Boys emerge from the shadows ahead of him. When MacGyver approaches them, he falls through a trapdoor and into a cargo net. The Tough Boys set a bomb on a chair in front of him, just out of reach, and make their escape. With three minutes left, MacGyver manages to swing over, grab a piece of copper piping from an exhaust fan, snare an extension cord, and lasso the chair. He grabs the bomb but is unable to defuse it as the timer counts to zero... and nothing happens.
MacGyver brings Manny in, and his friend figures that the Tough Boys were trying to scare him off. When he suggests that MacGyver let the police handle it, MacGyver points out that the snare net is a Force Recon design. When Manny notes that anybody could get the design out of a manual, MacGyver insists that Force Recon doesn't publish the design. Manny snaps at him, asking if MacGyver wants to become the cop, but MacGyver insists on seeing Hines.
At Hines' house, MacGyver finds the door open. He goes inside and Hines ambushes him, holding a gun to his head. The ex-Marine wants to know why MacGyver is dogging him. MacGyver shares his suspicions but Hines insists that he wouldn't recruit anyone to fight his battles for him. He insists he doesn't break the law and accuses MacGyver of being an idealist without a clue of what goes on in the streets. MacGyver stands by his beliefs and explains that the trap was set anticipating he'd pick the locked route. They both figure that means someone who knows MacGyver planned the operation.
Coco meets with his friends and tells them that The Man is going to meet with them and they have to be focused. The Man arrives: Manny. He tells them that they're going to perform one last major burndown at a cannery and then call it quits.
Hines figures that Manny, who served with him in Vietnam in the Marines, is the one responsible. Manny's daughter became an addict and his granddaughter is a crack baby, and Manny's wife left him because of the strain. They go to find Manny and stop him.
Manny reviews the assault plan on the cannery with the four boys and tells them that once they're done, they can go home and never look back. While they're attacking the cannery, he'll go after Dennis on his yacht and finish him off. The five of them vow to avenge the lives of their family members that they've lost to drugs. Manny returns home and finds Hines and MacGyver waiting for him. When they tell him what they know, he draws a gun and forces them into the garage, telling them that he'll be all over the news at 3:00. He bars the door and leaves. Once Manny is gone, MacGyver uses a lawn mower starter cord and paint can handles to make a grappling hook. He lowers it through the transom, snags the bar, and lifts it up so they can get free.
Dennis tells Harris and Myron that he's leaked word that the cannery is a major drug distribution center. He orders them to go there and set up an ambush to finish off the Tough Boys once and for all. When the teenagers arrive, the two men open fire and shoot Coco and Hector. Angel and Sinclair get them to cover as MacGyver and Hines arrive. They manage to subdue Myron and Hines takes his Uzi. Harris pins them down and Hines prepares to shoot back, but MacGyver stops him. He hooks up a fire hose to a hydrant and threads it through a ladder, and then has Hines use the Uzi as a wrench to open the hydrant valve. Using the ladder, MacGyver aims the water and blasts Harris off of his perch. They discover that Coco is dead. MacGyver goes to call the press, figuring that Manny informed them of what he was doing at 3:00.
Manny has taken Dennis prisoner on his yacht and wired the ship with explosives. The press has assembled and Manny informs them that he plans to kill Dennis at the cost of his own life. He reads a letter from his daughter talking about how she became addicted to crack. Hines and MacGyver arrive and board the yacht, refusing to let Manny kill himself. They tell him about Coco's death and insist that they can't afford to lose Manny as well. They approach their friend and Manny finally hands over the trigger device. Hines promises that they'll help Manny see it through... together.
Later, Hines is teaching his class and notices that MacGyver is less than impressed. He invites MacGyver to take over, and MacGyver runs the class through some easier stretching exercises, and has Hines join in.