At the Santa Luisa Mission, Father Jim leaves for his round before attending a public hearing meeting. He tells his assistant Rachel to tell MacGyver "black and blue" if he stops at the mission. As Father Jim walks down the streets, two men attack him and drag him into an alleyway to rob him. A homeless man, Danny, overhears them talking and sees them taking everything that Father Jim has.
At the public hearing, many of the locals are complaining that the homeless problem is raising property values and leading to increased crime on the streets. MacGyver arrives and Rachel admits she's worried that Father Jim is running late. She tells MacGyver "black and blue" and he explains it's a code word they used when they played hockey and one of them needed the other's protection from the opposing team. The chairman interrupts to tell the attendees that Father Jim has been taken to the hospital in critical condition after he was mugged. MacGyver and Rachel go to the hospital but Father Jim can only mutter a few cryptic words about papers. Outside, Lt. Rhone meets with MacGyver and admits that they don't have much to go on. However, he warns they don't have many lines of communication into the homeless community. The doctor comes out to tell them that Father Jim passed away.
Three days later at the funeral, Aaron Sandler stops to talk to Rachel and express his condolences. He explains that he has some of the homeless work at his plant and he was just starting to learn about Father Jim. The pallbearers place Father Jim in the hearse and Rachel points out Doc, a homeless man. She explains that Doc was one of Father Jim's favorites. She wonders if the police will find the killers and wonders if they care. MacGyver insists they do but explains that the homeless are afraid to talk to the police. He realizes that they do talk among themselves and gets an idea.
As one of the muggers, Mooney, goes through his belongings at a local gathering spot for the homeless, MacGyver comes by dressed as a homeless person. He asks for Doc and finds a cardboard box with a photo of Father Jim and Doc together. Doc arrives and shoves him to the ground and asks what he wants. MacGyver introduces himself as Grazer and says he's looking for Doc. He says that Father Jim asked him to find Doc. Mooney hears the conversation and leaves. Doc has a brief asthma attack and MacGyver explains that Father Jim said to find him and Danny. Doc agrees to take him to Danny but warns that the boy can barely take care of himself. Danny, who can't speak, was put out on the streets after cutbacks in mental institutions. Father Jim took Danny under his wing and helped the boy to recover. Doc figures that Father Jim's attackers aren't locals because the priest brought food and clothing for the homeless. They find Danny, who has been near-catatonic since the night of Father Jim's death.
Doc takes MacGyver over to Danny and then leaves on what he claims is an appointment he can't be late for. MacGyver tries to get through to him without success and goes back to Doc's shelter. He finds Doc talking with a girl, Allison. Doc explains that Allison is his daughter and she comes down once a week to see him even though her mother doesn't want her to. Doc has another asthma attack and explains that he used to be a high school English teacher. Then he had a breakdown and lost everything.
That night, MacGyver brings Danny some more food. As they cook, Danny sees a newspaper article on Father Jim's death and freezes up. MacGyver realizes that Danny saw the mugging and that one of the men in the photo was responsible. Danny finally points out Mooney, who was at the funeral, and explains that there was a second man involved. MacGyver gets Danny to mime that a third man in an expensive car picked them up. Doc arrives and identifies the man as Mooney, a troublemaker. He agrees to go through Father Jim's records to see if he can find a reason for the priest's murder.
MacGyver goes out to look for Mooney and sees a man stab him on the street. MacGyver goes after the attacker, who runs down the street and climbs a fence into an alleyway. MacGyver goes after the man and a guard with a security dog confronts both of them. The attacker insists MacGyver attacked him and the guard believes him and sends the attacker to make a call while the guard holds MacGyver prisoner.
The next morning, Lt. Rhone gets MacGyver out of jail. The lieutenant notes that going undercover wasn't a good idea and that they've closed the case. They've identified Mooney as an ex-con living on the streets and figure he killed Father Jim alone. Mooney had Father Jim's clothing and identification, but MacGyver insists that the man who killed Mooney deliberately attacked him. He says that Danny identified the killers but he'll never stand up in court as a reliable witness. MacGyver figures their best bet to find more evidence is for him to go back undercover. As he leaves, the killer, Riker, is in a car across the street with Sandler. Riker warns Sandler that MacGyver can identify him and Sandler recognizes him from the funeral.
At the mission, Doc is going through Father Jim's files when MacGyver arrives. Rachel is there and blows MacGyver's cover, and Doc realizes that he's been deceived. He has another asthma attack from the stress and wonders if he can trust MacGyver. MacGyver explains that they're both friends of Father Jim and they'll need to work together to solve the priest's murder. Rachel is called away to meet with a visitor: Sandler. Meanwhile, Doc shows that Danny was kept on the rolls of the mental hospital for a year after he was released. They also kept his medical checks along with hundreds of other discharged patients. Doc has checked with Dr. Kessler, who used to run the mental hospital. A man named Rooter owned the hospital, and every hospital he owned had a suspicious fire right before he purchased them. Rooter bought them cheap, stole the patient checks, and then disappeared once the scam had run its course. There's no description of Rooter and no photos in the hospital brochures. MacGyver has Doc continue to go through the files while he goes to the library and sees what he can find.
As MacGyver leaves, he runs into Rachel and Sandler. Rachel explains that Sandler has just made a major donation. Outside, Riker follows MacGyver while Rachel mentions that Danny saw Father Jim's murder. Sandler asks Rachel to get Danny and as many other homeless persons as possible to show up and he'll get a truck there in an hour with warm clothing.
At the library, MacGyver goes through magazines and finds an article on the hospitals.
The homeless people gather to get the coats from Sandler. Danny comes by and Rachel calls him over. Sandler takes Danny a coat and explains he was a close friend of Father Jim.
MacGyver photocopies the magazine article and realizes that Sandler is Rooter. He leaves but Riker is waiting for him and takes him captive at gunpoint. He takes MacGyver into an abandoned construction site. As Riker prepares to shoot MacGyver, MacGyver backs through a support, grabs a beam, and slams it into Riker, knocking him out. The only rope is too big so MacGyver uses a staple gun to staple Riker to the wooden flooring boards. He then uses some rope to tie Riker up
At the mission, Doc is helping Rachel when MacGyver returns to find Danny. They spot Sandler taking Danny away and MacGyver explains that Sandler is Rooter. He pursues Sandler on a motorbike as the businessman takes Danny to his plant. As MacGyver finds a way in through a transom, Sandler shows Danny around the plant. He wonders how much Danny knows but figures it doesn't matter if Danny can't tell him. Using a handkerchief, Sandler takes out a knife and says it was used to punish one of the men who killed Father Jim. He tells Danny to pick it up and the homeless man reluctantly starts to. MacGyver interrupts them and tells Danny to get away. Sandler goes for his gun and Danny sees him. He manages to yell a warning and he and MacGyver both duck for cover. MacGyver grabs a rubber glove and ties it to a gas valve, then opens up the valve and uses a light bulb to heat the gas. Finally he grabs some clay and throws it at the glove as Sandler walks past it. The bulb breaks and the spark sets off the gas, causing an explosion that knocks Sandler out. MacGyver finds Danny and assures him that Sandler isn't going to hurt him any more.
Later, MacGyver and the others say goodbye to Danny, who is going to a mental care facility with Dr. Kessler. Danny, who can now speak, thanks MacGyver for his help. Doc is going to help Rachel run the mission. As Doc goes inside with his daughter, Rachel thanks MacGyver as well. He worries that others may have fallen through the safety net and refuses to accept that anyone has to suffer that way.