MacGyver is arriving home at his new houseboat and chatting with his neighbor Lynda when Pete arrives to tell him that Jimmy "The Eraser" Kendall's photo is in the newspaper, due to a story about his baseball team. Pete figures he's in danger as soon as the Mob spot the photo and realize Jimmy isn't dead. Jimmy and his minor league team are arriving at Shoreline Stadium and MacGyver heads out to meet them.
Jimmy's team arrives at the stadium and settles in. Jimmy assures his pitcher Dave Malone that it's just like playing at home.
Papa Chuck's main hitter, Ralph, is called to the dock to meet with Papa Chuck's successor, Paul Webber. As Webber praises Ralph's abilities, Ralph's partner Sal reads a newspaper and realizes Jimmy is still alive. He tries to tell Ralph, who brushes him off. Once Webber has left, he finally tells Ralph that Jimmy is still alive and Ralph failed. If the Family finds out, Ralph will be in serious trouble. Ralph vows to finish him off.
MacGyver arrives at the stadium where Jimmy has called in Hank Aaron for Dave to warm up against and relax. Hank hits a run into the stands off of him and Jimmy tells Dave to ignore who he's pitching against and just do what he does best. Dave manages to strike Aaron out. Once the team heads back to the lockers, MacGyver greets Jimmy and tells him what's happened. Jimmy admits it's bad timing and MacGyver tells him he has to get a new identity and a new life. Jimmy is reluctant but MacGyver convinces him he doesn't have a choice. Ralph and Sal arrive and chase them into a men's restroom. The hitmen come in and find one closed stall. Ralph fires through the door but discovers they've slipped out the back. They run out to the stadium and bar the door with a mop, and then MacGyver uses a fire hose to slide down a wire so they can escape. Ralph isn't worried: he knows where Jimmy's daughter is.
MacGyver goes back to his houseboat with Jimmy. Meanwhile, Jimmy's grandson Brian comes home and admits to his mother Susan that he didn't get a chance to play baseball. Ralph arrives and tells her he has a message from her father.
Pete arrives to tell MacGyver and Jimmy that they didn't find anything at the stadium. MacGyver figures that Ralph and Sal can't tell their bosses what's going on. Pete wants to move Jimmy to Montana and Jimmy wonders if it's worth it. He asks to make a call so he can reassure Dave. Pete lets him make the one call and warns him not to tell anyone where he is. Once Pete leaves and MacGyver goes to take a shower, Jimmy talks to Dave, who tells him that Ralph left a message about Jimmy's daughter and grandson. Dave passes on the phone number Ralph left, and Jimmy claims he has to call another player at the hospital. He calls Ralph, who is at a cannery plant at the docks with Susan and Brian. Ralph tells him to come alone. Once he hangs up, Jimmy fakes the call to his player as MacGyver comes back down. Jimmy throws away the paper he wrote the phone number on and MacGyver tries to reassure him. Jimmy talks about how he went to church as a child and calls the priest, Father Kowalsky. He arranges to meet with the priest.
MacGyver drives Jimmy to the church where he goes into the confessional booth. Kowalsky, who isn't a priest, has a gun for him and Jimmy hides it and goes back out. He genuflects at the altar but MacGyver notices Kowalsky doesn't when he goes by. Jimmy admits he obtained a gun and explains that Ralph snatches Susan and Brian, the grandson he never knew he had. MacGyver suggests they call the cops but Jimmy figures Ralph will kill his family if there's any hint of police involvement. He'd rather die as long as his family dies. MacGyver promises no police but insists on helping. Jimmy knocks him out and then runs out before MacGyver can catch him.
MacGyver goes back to his houseboat and checks the paper he saw Jimmy throw away earlier. He calls Pete and tells him what happened, and has him trace the call.
At the cannery, Ralph tells Sal to hide outside while Susan explains that her father was an insurance salesman who died when she was three and he's making a mistake. Ralph assures her that her father is alive, but not for long.
MacGyver arrives at the cannery, climbs over the fence, and scales the roof. Meanwhile, Jimmy slips in from a different direction and rolls a bottle out so Sal sees it. When the mobster goes to investigate, Jimmy gets the drop on him and demands to know where his family is. Sal tells him they're in inside with Ralph and Jimmy tells him to lure Ralph out. Sal steps out and calls to his partner, saying he's saw someone and Ralph needs to come out. In response, Ralph shoves Susan and Brian out at gunpoint. MacGyver climbs to a crane overhead while Jimmy tries to negotiate, trading Sal for Jimmy's family. Ralph isn't interested and tells Jimmy to make up his mind. Jimmy has no choice but to give up his gun. Meanwhile, MacGyver drops a net from the crane onto Sal, drops down on the rope, and tackles Ralph. Jimmy gets his family into the cannery plant while Ralph takes out MacGyver. He knocks him off the dock and into the water below, and Sal tosses Ralph his gun. Ralph shoots MacGyver, who sinks below the water.
Jimmy realizes all the doors out of the cannery are locked. As he and his family settle down, Ralph and Sal start searching the plant. Jimmy tries to explain he tried to keep her out of the entire thing and did it for her and her mother. She doesn't believe it.
Outside, a badly wounded MacGyver crawls out of the water and up onto the dock.
Jimmy hears the mobsters searching the building and confirms they're coming after him. He tells Brian to get his mother out the window while he distracts them, and not to stop for anything. he says goodbye to his grandson and then goes back after Ralph and Sal.
MacGyver stumbles into the plant, leaking blood.
Ralph tells Jimmy to come out, informing him that MacGyver is dead. Jimmy starts making noise while Susan and Brian break through the window.
MacGyver collapses, and spots two fishing pikes nearby. Meanwhile, Jimmy yells out to Ralph to draw his attention. Ralph and Sal corner him and refuse to let Jimmy's family go. Ralph shoots him in the shoulder to force him to reveal where Susan and Brian are. MacGyver grabs the pikes and follows the gunshot. Jimmy refuses to talk but Ralph figures Jimmy's screaming will bring them out. He tells them his family has already escaped, but Ralph figures they'll run them down. As he prepares to fire, MacGyver arrives and throws a fishing pike into a nearby steam valve, blinding the hitmen. He then clubs them unconscious with the other pike. Jimmy thanks him for his help.
Later, Jimmy is at MacGyver's houseboat with Susan and Brian and tells his grandson how to play baseball. He promises that he'll be there to show him how to do it and they head out for a baseball game.