Father Jim leaves the Santa Luisa Mission for his nightly rounds delivering food to the homeless. He tells his assistant, Rachel, that he'll be at the public hearing on time and to tell his friend MacGyver "black and blue" if he stops at the mission. As he goes down the street, a homeless man, Mooney, holds him up. When Father Jim tries to appeal to him, Mooney's partner Riker comes up from behind and knocks the priest out, and the two men drag their victim into an alley. A homeless boy, Danny, is sleeping nearby. He wakes up at the noise and sees the entire thing.
MacGyver arrives at the public hearing as the locals complain the homeless problem is ruining the property values and causing an increase in crime. He talks to Rachel, who passes on Father Jim's message and admits she's worried that he hasn't arrived yet. MacGyver explains that the phrase was a codeword he and Father Jim used when they were playing hockey together and needed to protect each other from the opposing team. The chairman receives a message and informs the attendees that Father Jim is in critical condition after the mugging.
MacGyver and Rachel go to the hospital and talk with the dying Father Jim, who says to check his papers. They go outside and meet with Lt. Rhone, who admits they don't have much to go on and the homeless community isn't willing to talk to the police. The doctor comes out to tell them that Father Jim has passed away.
Three days later, MacGyver and Rachel attend the funeral and meet with Aaron Sandler, a local businessman. He expresses his condolences and explains that he had just met Father Jim when they started working together to find employment for the homeless at Sandler's plant. Among the many homeless persons present are a guilty Mooney. Father Jim's friends serve as pallbearer and Rachel points out Doc, one of the priest's closest friends. Another was a boy, Danny. MacGyver explains that the police want to help but the homeless don't trust outsiders, but he has an idea.
MacGyver, wearing old clothing, goes to a local gathering of homeless beneath a bridge. Among the people present are Mooney. MacGyver finds the cardboard box that Doc uses for a shelter and spots a photo of him and Father Jim together. Doc arrives and demands to know what he wants and then panics, having an asthma attack. MacGyver manages to calm him down and explains that Father Jim told him to find Doc and Danny if anything happened to him. Doc agrees to lead MacGyver to Danny, but warns that due to mental problems the boy can barely talk. Mooney, listening in, leaves after noting MacGyver's interest.
As they look for the boy, Doc explains that Danny was in a mental institution until cutbacks forced them to put him out on the streets. The priest did what he could for Danny. Doc insists that no one among the homeless would have mugged Father Jim because of his efforts on their behalf. They find Danny and Doc leaves for what he claims is an appointment. MacGyver tries to befriend Danny but the boy refuses to say anything and barely acknowledges his efforts. MacGyver goes back to Doc's box and sees the man at a distance, talking to a young woman who quickly leaves. Doc comes over and explains that the woman is his daughter Allison, and she comes to visit him once a week even though her mother disapproves. The stress brings on another asthma attack. Once Doc recovers, he explains that he used to be a well-paid English teacher with a home and family until he had a breakdown. He couldn't afford the medical bills, lost everything, and his wife divorced him.
That night, MacGyver forages for food and brings it to Danny. The boy starts to warm up to him but as MacGyver cooks a meal, Danny notices a newspaper with a photo of Father Jim's funeral. He panics and MacGyver realizes that the boy recognizes one of the men in the photo from the mugging. He gets him to point out Mooney, and Danny mimes an explanation that there was a second man, and that both muggers were driven away by a third man in an expensive car. Doc finds them and explains that Mooney is a homeless ex-con known for causing trouble. MacGyver convinces him to go through Father Jim's papers and use his knowledge and experience to see if he can find anything useful.
MacGyver starts searching for the streets. He finds the man just in time to witness him be stabbed and killed by his partner, Riker. MacGyver chases Riker into an alleyway but a security guard catches both of them. Riker insists that MacGyver tried to mug him. The guard, prejudiced against the homeless, believes Riker and tells him to go call the police while he holds MacGyver there.
The next day, Rhone gets the situation cleared up and gets MacGyver out of jail. He explains that with Mooney's death, his department has closed the case. The dead man had Father Jim's wallet on him and was wearing his stolen shoes. MacGyver explains that there was an eyewitness who identified two other men, but admits that Danny's testimony won't stand up in court and they need solid evidence. MacGyver heads out of the station house and back to the streets, unaware that Riker is watching him from across the street with his accomplice: Sandler. Sandler realizes who MacGyver is from the funeral and tells Riker to take care of him.
MacGyver goes back to the mission and meets with Doc. Rachel is also there and says MacGyver's name, and Doc realizes that he's been tricked. He has another asthma attack as he panics and MacGyver calms him down, explaining that they're both friends of Father Jim and regardless of where they live or how much money they have, they both want the killers brought to justice. Doc calms down and shows MacGyver what he's found, while Rachel goes to meet with a visitor: Sandler.
According to Father Jim's files, the mental hospital where Danny was staying kept his name listed as a patient up to a year after he left. The files show that the hospital owner, a man named Rooter, did the same thing with hundreds of other discharged patients, keeping their medical checks for himself. According to Dr. Kessler, the woman who ran the hospital, Rooter arranged fires at the hospitals, bought them up cheap, and then used them to run his scam before disappearing. There are no photos or description of Rooter. MacGyver has Doc continue to look for information while he goes to the library to check the newspapers for any photos.
In the hallway, Sandler offers Rachel a major donation. As MacGyver leaves, Rachel explains that he's working with Danny to identify the killers. Sandler offers her a truckload of warm coats for the homeless community and asks Rachel to get Danny and all the others there to collect them.
An hour later, the homeless community gathers to collect the coats. Danny arrives and Rachel identifies him for Sandler, and then calls the boy over.
MacGyver finds a newspaper of photo of Rooter and confirms that he's actually Sandler. As he leaves, Riker grabs him and takes him to a nearby construction site to finish him off. MacGyver manages to stun him with a scaffold rail and then uses a staple gun to pin Riker to the wooden floorboards. He goes back to the mission just in time to see Sandler taking Danny away in his car. He tells Doc and Rachel to call the police and goes after him on a motorbike.
Sandler takes Danny to his manufacturing plant. Making sure not to leave his fingerprints, Sandler offers Danny the knife that Riker used to kill Mooney, and says that it was the weapon used to punish the man who killed Father Jim. Danny starts to take it but MacGyver slips in and tells him not to. Sandler reaches for the gun in his belt to shoot MacGyver. Seeing his new friend in Danger, Danny manages to overcome his speech inhibition and yell a warning. MacGyver ducks for cover and Sandler goes after him. Spotting a rubber glove, MacGyver attaches it to a gas valve, release the gas, and hangs up a light bulb nearby. He then ducks behind some shelves and finds some wet clay used to make toilets. When Sandler comes by and finds the glove, MacGyver throws the clay, shattering the bulb and sparking off the gas. The concussion knocks out Sandler, and MacGyver assures Danny that the businessman will never hurt anyone again.
Later at the mission, MacGyver, Doc, and Rachel say goodbye to Danny, who is going back to the mental hospital with Dr. Kessler. Danny is able to say goodbye to his friends and thank MacGyver for his help. Doc's daughter Allison is there and Rachel assures him that he can help her carry on Father Jim's work. As doc goes inside with his daughter, Rachel thanks MacGyver. He wonders if they're doing enough and insists that they can never accept what has happened to the homeless.