Black-clad vigilantes calling themselves the Tough Boys launch a series of military-style attacks on crack houses in their neighborhood. After planting explosives up a crack lab, they realize that one of the dealers was still inside. Before they can go back in to rescue him, the place goes up.
At the Challengers Club, MacGyver's old friend Manny, a former cop, is helping out with the new SELF program. He explains that he moved to Nebraska but eventually sold the farm and moved back to get his old job back. Thanks to Cynthia Wilson and Rutherford Hines, the Club's enrollment has tripled and the Phoenix financed self-esteem program is proceeding under Hines' guidance. Manny explains that his wife divorced him because she couldn't handle the pressures of his job. As they go in, Manny asks MacGyver to keep an open mind about Hines. As they enter, Hines, a former USMC officer, has the members in karate uniforms and is running them through drills. Manny explains that Hines keeps pushing until they get out of the gangs and start getting better grades. MacGyver sees Coco Hubbard, a former gang leader who Manny explains left the gang to join Hines' program. The class is interrupted when a teen, Angel Royas, arrives late, drunk and playing loud music on his boom box. When Hines tells him to shape up, Angel tries to attack him and Hines dunks his head into a bucket of water. MacGyver intervenes and Angel stalks off, insisting he's no one's soldier.
Hines gives the class a break and confronts MacGyver outside. He warns MacGyver that no one interferes with his kids or undercuts his authority. MacGyver warns that what Hines was doing was excessive. Manny tries to intervene but Hines insists that MacGyver is just passing through and he has to deal with the violence on the streets every day.
On his yacht at the pier, drug lord Dennis orders his men to take out the Tough Boys, who are getting news coverage thanks to their high-profile attacks on crack warehouses.
At the club, MacGyver hears Coco discussing Angel with two of his friends, Hector and Sinclair. Coco says that Angel will be okay. They tune in to a newscast on a Tough Boys piece that reveals that there has been a fatality for the first time. They quickly turn off the newscast but it's clear they're involved.
Coco, Hector, and Sinclair grab Angel, who is packed and ready to leave. Angel puts up a fight and insists they should have rescued the crack dealer, who was the same age as his brother when he died. Coco says that he lost a cousin to drug violence and understands, and promises there won't be any more dying. Angel agrees to join back up with them and Coco takes a punch to get even. As they leave, Coco tells Angel that the man in charge is sending them after some rich boys who are pushing drugs into the neighborhood.
Manny investigates one of the Tough Boy burndowns with MacGyver. MacGyver suspects that Hines might be tied in with the Tough Boys but Manny says he has plenty of organizations that fit the profile and Hines couldn't be involved. As MacGyver leaves, Manny warns that a drug boss has put up a reward for info on the Tough Boys and MacGyver should avoid being caught in the middle.
Dennis meets with his men Harris and Myron, who have narrowed the Tough Boys' leader down to one of three possibilities, including Hines.
MacGyver returns to the club and notices that Angel has a black eye. He tries to talk to the teenager about the Tough Boys but Hines interrupts and sends Angel back to work. He wonders if MacGyver thinks he hit Angel, but MacGyver notes that Hines uses the wrong hand. Hines warns him off and leaves. Once MacGyver goes inside, Coco and the others worry that MacGyver is getting too close and their leader told them to tag him.
Later, MacGyver is driving down the street when one of the Tough Boys leaps across the back of his truck and then runs into a nearby building. MacGyver figures it's a trap and goes inside. One of them runs upstairs and turns on a boom box, MacGyver goes up and finds a locked storage cage. He picks it and goes inside and the Tough Boys show themselves and then run away. When MacGyver follows them, he falls through a trapdoor and into a cage, dropping his Swiss Army knife. The Tough Boys then set a chair in front of him with an explosive set to go off in three minutes.
MacGyver swings over toward the chair and tries to grab the bomb. Unable to quite reach, he swings to the side and grabs an extension cord dangling from the ceiling. When he's unable to use that, he swings over to a fan and grabs some copper tubing, and uses it as a hook to grab the extension cord. He then lassos the chair and pulls it close enough to hook the bomb with the tubing. It reaches zero before he can shut it off but nothing happens.
MacGyver shows the bomb to Manny and the police. Manny figures they were trying to scare him off and suggests MacGyver let the police handle it. MacGyver points out that the snare net is Force Recon and they don't make manuals. Manny snaps at him but MacGyver insists on going to see Hines at his home. Hines isn't there and MacGyver looks around. Hines gets the drop on him and wants to know why he's dogging him. MacGyver says he has nothing to worry about if he isn't the Tough Boys' leader. Hines denies it, insisting he doesn't let kids fight his battles and he doesn't break the law. He accuses MacGyver of being an idealist but MacGyver insists that discipline isn't an issue unless it's clumsily administered. When MacGyver explains that the trap was put in front of the locked door, he and Hines figure that whoever set the whole thing up knows him very well.
Coco tells the others that they need to be focused for when their leader gives them orders. The leader arrives: Manny. He's got plans for their last burndown, which will be a major one at a cannery.
Hines reveals that he served with Manny in the Marines and MacGyver figures that he could have provided the Tough Boys with all the training they needed. Manny's daughter died due to drugs and they go to talk to him.
Manny goes over his plan with the Tough Boys and tells them to wrap things up at the cannery, go home, and never look back. Manny plans to go to the yacht to take down Dennis and they all take a vow on the lives of the family they lost to drugs.
Manny returns home and finds MacGyver and Hines waiting for him. He tries to bluff it out and when that doesn't work, he draws a gun and tells them he's going to take out Dennis and make sure it's all over the news at 3 o'clock. Manny forces them in at gunpoint and insists that the law doesn't care about crack users. His granddaughter was a crack baby after his daughter became addicted. Manny locks them in the garage with a drop bar and leaves. MacGyver uses the wire handles from paint cans and has Hines sharpen them while he pulls the starter cord off of a lawn mower.
Dennis tells his men that he's put out plans for a major drug deal and that they need to set an ambush at the cannery when the Tough Boys take the bait.
Using the paint cans as a grappling hook and the starter cord as a rope, MacGyver snags the bar, lifts it, and opens the door.
Harris and Myron get ready to catch the Tough Boys in a crossfire. The teenagers arrive and Angel spots them. Coco and Hector go down and Angel and Sinclair drag their comrades to cover. MacGyver and Hines arrive and Myron goes to investigate. Hines and MacGyver split up and Hines circles around to distract the thug while MacGyver knocks him off the pier. Hines picks up the man's Uzi while Harris fires at MacGyver. Hines prepares to return fire but MacGyver stops him and then uses the Uzi to loosen the valve on a nearby fire hydrant. MacGyver then grabs a ladder and a fire hose and threads the hose through the ladder. Hines turns on the water and MacGyver knocks Harris off his post. Angel arrives to take them to Coco, who is dead. Sinclair tells them that Manny went to take out Dennis and MacGyver figures they can check with the press since Manny said he was going to commit a public execution
At the docks, Manny has boarded Dennis' yacht and armed himself with explosives. He has called in the press and tells them that he plans to kill himself and Dennis. He reads the press a letter from his daughter telling of her addiction. MacGyver and Hines arrive and try to stop him. They board the yacht and refuse to let Manny blow himself up without taking them out as well. They tell him that Coco died and it won't do any good for them to lose Manny as well. Hines tells him that he has a granddaughter to take care of and Manny gives up the trigger device. Hines promises that he and MacGyver will see him through it... together.
Later, Hines teaches his self-respect class and notices MacGyver frowning. MacGyver suggests that Hines might start with some sensitive stretching exercises and offers to take over. He has Hines join them and puts them through some easy stretching exercises.