MacGyver is flirting with Lynda, the new neighbor living next door to his houseboat, when Pete arrives to show him a newspaper article about a Triple AAA baseball team, the Bluebirds, that are playing at Shoreline Stadium. The article has a photo that shows Jimmy Kendall, aka "The Eraser," the hitman that MacGyver helped get into the Witness Protection Program. Pete figures that it won't be long until someone in the Mob sees the photo and realizes that Jimmy is still alive. MacGyver heads down to the stadium to rescue Jimmy.
The Bluebirds arrive at the stadium and Jimmy tells his starting pitcher Dave Malone to relax and just treat it like any other stadium.
Mob boss Papa Chuck has just died and his successor, Paul Webber, is taking over. He meets with Ralph, the mobster who worked with Papa Chuck and supposedly eliminated Jimmy. Webber praises Ralph for his work and assures him that he'll be moving up in the Organization and Ralph is eager to assure Webber he can handle it. However, once Webber is gone, Ralph's partner Sal sees the newspaper article and tells Ralph that Jimmy is still alive. Ralph realizes that if Webber learns he screwed up, he'll be eliminated himself. The two mobsters head to the stadium to finish Jimmy off before anyone else learns about him.
MacGyver gets to the stadium while Jimmy is having Dave warm up against Hank Aaron. Dave is initially nervous but manages to overcome his fear and strikes out the home-run king. Once the team has gone back to the locker room, MacGyver approaches Jimmy and tells him what's happened. Jimmy is reluctant to give up his new perfect life but soon realizes he doesn't have any other choice. However, Ralph and Sal arrive and come after them. MacGyver and Jimmy try to evade them and eventually flee to the upper stadium tier and temporarily bar the door. As Ralph and Sal break through, MacGyver uses a fire hose as a strap so he and Jimmy can slide down to the stadium floor and escape before the mobsters can catch them. Sal worries they won't be able to kill Jimmy but Ralph has a trump card: he knows where Jimmy's daughter and grandson live.
At the home of Susan Walker, Susan's son Brian arrives home from baseball. He's covered in dirt but admits that the coach didn't give him a chance to play. Brian tells his mother that he slid home after the game so it'd look like he played. They're interrupted when Ralph arrives and tells Susan that he has a message from her father.
Pete meets with MacGyver and Jimmy at the houseboat and tells them the police didn't find any sign of the mobsters at the stadium. They figure that Ralph has to kill Jimmy on his own so he doesn't reveal how he screwed up the first time. Jimmy argues that he'd rather be dead than lose his current life, but finally seems to accept the situation. However, after Pete leaves and MacGyver steps out to take a shower, Jimmy calls the stadium to check on Dave. Dave tells him that Ralph left a message about Susan and Brian, and a phone number to call. Jimmy writes down the number and calls Ralph, who is holed up at a cannery plant that belonged to Papa Chuck. Ralph tells Jimmy to come alone. As MacGyver comes in, Jimmy throws away the number and then says he wants to visit a church for confession
MacGyver drives Jimmy to the church where Jimmy meets with the supposed priest, Father Kowalsky. Kowalsky is a friend of Jimmy's and slips him a gun in the confessional booth. However, when Kowalsky leaves, MacGyver notices that he didn't genuflect before the altar and realizes something is up. He confronts Jimmy, who admits that Ralph has his family and that he doesn't have any other choice. MacGyver promises to help and not call in the authority, but Jimmy knocks him down and runs out, escaping down the street before MacGyver can find him. Remembering the paper that Jimmy threw away, MacGyver goes back to the houseboat, gets the phone number, and has Pete trace it.
Ralph has Sal wait for Jimmy outside the cannery. Susan thinks he's making a mistake because her father was an insurance salesman who died when she was three. Ralph explains that her father is still alive, but Ralph will soon take care of that.
MacGyver sneaks into the cannery and climbs up the roof. Jimmy comes in separately and easily gets the drop on Sal. He forces Sal to trick Ralph into coming out, but Ralph figures it's a trap and brings out Susan and Brian as hostages. Jimmy offers to exchange Sal for his family, but Ralph refuses to deal. Jimmy has no choice but to give up his gun, and Ralph prepares to kill him. MacGyver drops a net from an overhead crane, tangling up Sal, and then drops down and tackles Ralph. Jimmy gets Susan and Brian into the cannery while Ralph gets the upper hand in the fight. Sal frees himself and tosses Ralph Jimmy's gun, and Ralph kicks MacGyver into the water and then shoots him. MacGyver sinks beneath the waves.
Jimmy realizes that they're trapped. He hides his family and then tries to explain to Susan that he abandoned her as a child because it was safer for her and her mother. She doesn't believe it, while Brian is happy to discover he has a grandfather.
Outside, MacGyver manages to crawl up onto the dock despite the stomach wound, and gets into the cannery. Meanwhile, Ralph and Sal search the cannery and Jimmy tells Susan and Brian that he'll distract the killers while they break through a window and escape. He says goodbye to Brian and then goes back. Ralph calls out to Jimmy that MacGyver is dead and he's next, and Jimmy creates his distraction.
While MacGyver finds two pikes, Ralph and Sal corner Jimmy. He refuses to tell them where his family is and Ralph shoots him in the shoulder to get him to tell so that they can eliminate the witnesses. Jimmy just laughs as he collapses next to a steam pump. When they realize that Jimmy won't talk, Ralph figures they can find Susan and Brian later and prepares to kill him. MacGyver arrive and throws one pike into a steam valve, blinding the killers. He manages to knock them out with the other pike and then collapses next to Jimmy.
Later, Jimmy and his family are at MacGyver's houseboat. Jimmy is preparing for a new life with his daughter, and is giving hitting tips to Brian. As they head out for a baseball game, Jimmy thanks MacGyver for his help.