MacGyver entertains Tommy Giordano with a robot toy as they wait outside a courthouse for the result of the divorce hearing between Tommy's parents, Mary Ruth and Richard. Mary Ruth has worked at the Phoenix Foundation since MacGyver joined the organization. Both parents are suing for custody of Tommy. Tommy doesn't totally understand what is going on and worries that the parent he is taken away from will stop loving him. The Giordanos come out and Mary Ruth tells her son that she'll be staying with him. Richard's lawyer warns him that his record of verbal abuse toward his son and even the judge cost him custody. Richard comes over and tries to make things better. Mary Ruth reluctantly agrees and Richard asks for a minute alone with his son. He tells Tommy to call if his mother starts acting hysterical again. As he leaves, Tommy mentions that he's going to the aquarium with MacGyver and Mary Ruth.
Mob kingpin Joe Catano meets with Paulie Rizzo, his right-hand man. Catano refuses to buckle under pressure from Peter Vicaro, a rival mobster who is selling drugs to kids. Despite Paulie's warnings, Catano refuses to compromise his principles and sell drugs that way. Richard comes in and Catano wonders why his nephew is showing up after all these years. Richard explains that he lost Tommy in the custody hearing, blames Mary Ruth, and asks for Joe's help to get his son back. Richard tries to manipulate Joe into helping, but his uncle is wise to his ways. However, Joe believes that a father should be with his son and agrees to help, saying he'll take Richard and the boy to Canada with him.
At the aquarium, MacGyver and Mary Ruth talk while Tommy runs to the next exhibit. Mary Ruth admits she's having trouble functioning on her own for the first time. As they catch up to Tommy, two of Joe's men grab the boy and run out the back exit. MacGyver goes after them but gets knocked down as they escape. MacGyver and Mary Ruth call in the police but the officer warns that there's nothing they can do in a civil matter, and Mary Ruth should wait a few days and see if Richard brings Tommy back.
Richard meets Tommy at Joe's manor and explains that they're going on a trip with Tommy's great-uncle to his ranch in Canada, and Mary Ruth knows about it. Joe, clearly pleased to see the boy after so long, comes in and chats with Tommy.
Mary Ruth and MacGyver meet with Pete, who explains Richard's connection to Joe Catano. Richard kept himself separate from his uncle's affairs and the Foundation never considered the connection a risk. Tommy calls to tell Mary Ruth goodbye before he goes on his trip to the ranch. Richard arrives and cuts the connection off.
As Joe leaves with his men, he introduces Richard to Paulie. Joe tells Paulie to meet them later at the ranch and leaves. Once he's gone. Paulie calls Vicaro and tells him that Joe has left for the ranch, and he'll make sure that Vicaro's killers get past security to kill Joe.
MacGyver and Mary Ruth go to Joe's estate where the FBI have already secured the place. The head agent, George Kaplan, tells them that they've tracked Joe's flight to Canada but there's nothing the FBI can do because it's a civil matter. He warns Mary Ruth that Vicaro has put a price on Joe's head and Tommy is at risk as well. MacGyver volunteers to recover Tommy but Kaplan warns that unless a parent is involved, it's considered kidnapping. Mary Ruth insists on going with MacGyver to save her son.
Joe arrives at his ranch in Alberta and explains to Tommy that someone is trying to take something from him that he worked hard to build. He makes sure Tommy understands not to go outside the gate. Meanwhile, MacGyver and Mary Ruth arrive and spot Tommy. They also spot two of Vicaro's killers watching the ranch. Inside the compound, Joe takes Tommy riding. Tommy describes how his mother is always upset when Richard is around and Joe begins to realize that Richard isn't telling him the truth.
MacGyver and Mary Ruth follows Vicaro's men to a local motel. They overhear the killers say that they're waiting for a call from their inside man. MacGyver pretends to be an astrology buff and convinces the motel clerk that the room he wants next door to the hitmen has special significance.
That night, Richard is calling overseas to set up a business in Vienna. When Tommy tries to talk to him, Richard snaps at his son and Joe angrily yanks the phone away from him. He demands answers and Richard explains he plans on moving himself and Tommy overseas. Joe insists that it's no life for Tommy but Richard is clearly only interested in himself. When Joe asks why, Richard defends his actions saying that Tommy belongs to him.
Once the killers settle in at their motel room, MacGyver starts to wire up the phone in his room to theirs so he can overhear the inside man when he calls. However, he needs to get into the mobsters' room so he can complete the connection. He tells Mary Ruth to make a diversion but the killers leave to get takeout food before she has to do anything. MacGyver slips into their room and goes to work.
Tommy is playing with a robot toy like the one MacGyver built for him, and describes his mother's friend. Joe privately assures the boy that he's going to send Tommy back to his mother, but he wants Tommy to call to talk with him from time to time.
MacGyver finishes the connection just as Paulie calls. The killers pull up and MacGyver is forced to hide in the shower. They miss Paulie's call and wait, so Mary Ruth fakes a loud fight. Next she runs next door and begs the two men for help. When they go over, MacGyver slips out. Mary Ruth claims that her abusive boyfriend must have run. The killers go back to their room and take Paule's call. He tells them that his man Tony is at the gate and will let them in when they arrive in a delivery van. As the hitmen leave in the delivery van, MacGyver tells Mary Ruth to call the police while he jumps onto the top of the van. Mary Ruth goes to the clerk and when he proves reluctant, she forces him to help.
The killers arrive at the ranch gates and Tony disposes of the other guard. MacGyver plugs the exhaust pipe using the dead guard's scarf and then sneaks into the ranch house. The killers finally clear the exhaust pipe and drive onto the grounds. They kill Joe's men while Paulie pulls out a gun and prepares to shoot Joe. MacGyver arrives and knocks Paulie out, and Joe recognizes him from Tommy's description. Richard comes downstairs with Tommy as Joe realizes who MacGyver is from Tommy's description. When Richard abandons Tommy and tries to escape, Joe knocks him unconscious.
MacGyver gets Joe and Tommy into the basement while the two killers from the motel break in. As they search the upstairs rooms, MacGyver takes Tommy's toy and mixes a small amount of alcohol, descaler, and ammonia in a dish-like compartment on its underside. Next he strips the wires and places them close to each other to generate a spark. Finally he places the toy at the base of the stairs and hides. The killers come down the stairs and accidentally knock the toy aside, separating the wires. MacGyver uses the remote to bump the toy into the stairs, knocking the wires back together. The killers spot Joe and MacGyver and prepare to shoot. MacGyver activates the spark, causing the chemicals to ignite into a thick cloud of smoke. He and Joe take the two men down. Outside, Mary Ruth pulls up and enters the house. She spots the third killer, Tony, and follows him to the basement. As he aims and prepares to fire, Mary Ruth knocks him out with a frying pan and Tommy runs to embrace his mother. Joe tells Mary Ruth to leave with her son, and he'll make sure Richard never bothers them again.
Later, Mary Ruth and Tommy meet MacGyver and Pete at the Foundation. As the two men play with Tommy's toy, she tells them that she's glad to have had the chance to learn how to function on her own. The guys warn her that compared to Tommy when he hits puberty, everything else she's faced is a piece of cake.