It's a dark and stormy night and MacGyver is at home working on a chemical experiment: developing a non-alcoholic version of eggnog. His grandfather Harry comes in out of the storm to meet for the hockey game that MacGyver invited him to come to. Harry isn't impressed with the eggnog, but notes that it's December 14, and that it's been twenty-five years. MacGyver notes that he's glad that Harry's there with him this year and they share a toast.
At the Phoenix Foundation, Victoria James and three men are parked in the basement garage waiting for a Susan Murphy to come out. Victoria informs the men that the Liberation Front hired her to blow up the building and assigned them to help. Once they're done, they'll never meet again. Meanwhile, MacGyver realizes that he left the hockey tickets at the Phoenix Foundation.
Murphy comes down to the parking garage and Victoria approaches her, gets her to say her name recorded on a hidden digital recorder, then guns her down. The men hide the body in the car and take her card key. Meanwhile, as MacGyver and Harry drive to the Phoenix Foundation, Harry remembers his wife teasing him about his stubble. MacGyver assures him that they'll get to the game in time. He remembers talking to his father about Harry.
The primary Liberation Front man, Phillips, is complaining that Victoria is an outsider and that she messed up an airport bombing. Victoria corrects him, noting that it was the Phoenix Foundation that thwarted her. They go up to the lobby and gets close enough to render the lobby guard unconscious. One man takes over as security guard and unlocks one elevator so they can go up to the lab on 8th. In the parking garage, MacGyver and Harry arrive and go up to the lobby.
Victoria and the other two men get through the lock using Murphy's key card and voice recording. She informs the men that she has to find the device first by going through the computer records before they can detonate it. Meanwhile, MacGyver talks to the (fake) security guard and signs in, and the guard releases the elevator and sends them up. MacGyver is suspicious when the guard lets Harry go in without an ID. The guard calls ahead and Victoria has her men hide in the stairwell with the equipment. MacGyver enters the lab and finds Victoria working, and she claims to be Susan Murphy and that she's working late on a Sunday in Demographics to meet a deadline. MacGyver goes to the office while Victoria locates the explosive device in the computer inventory file. She deletes the record and says goodbye to MacGyver. She then goes to the stairwell and has her security man shut down the stairwell and elevators to the eighth floor, as well as the telephones. She calls the Liberation Front and informs them that MacGyver, the one who stopped a previous assassination attempt, is in the building. She negotiates a new deal to dispose of him and tells the LF men to capture MacGyver because he's too dangerous to let go free.
MacGyver finds the hockey tickets and they head for the elevator. As Harry takes the tickets for safekeeping, MacGyver remembers playing checkers with Harry as a child and wondering why he wants MacGyver to call him "Harry." Harry insists that "Grandpa" is a name for an old man. MacGyver discovers the elevators are locked off and remembers that Victoria was wearing lipstick, but there wasn't any on her cigarette. He also remembers that Demographics is on the 4th floor. They head for the stairwell and see Phillips coming up. MacGyver retreats back to the 8th floor and hides as Phillips come up, but Harry knocks over an ash tray stand. They duck into the stairwell and go down to the 4th floor. MacGyver rigs the hydraulic door hinge to slow down and lets it slowly shut as they go down to the 3rd floor. Phillips sees the door closing and figures they went onto the 4th floor and goes after them.
Victoria and the other LF man, Fred, go to the lab and find the explosive device. Meanwhile, MacGyver and Harry get to the lobby only to find the door is locked: the fake guard has put a club-type floor jam, a "New York lock," on it. They go up to 3rd floor and MacGyver tries to call Pete, only to discover the lines are dead. Meanwhile, Phillips gets down to the lobby and starts searching the floors above again.
Victoria activates the bomb and explains to Fred that she wanted to use the device to destroy the building to eliminate it so it couldn't be traced back to her. Meanwhile, MacGyver and Harry get to the lab and Phillips starts to search the floor they're on. MacGyver collects a battery, an iron faucet, and some copper wiring from a high-security vault. As they work, Harry notes that he's usually up on the farm and MacGyver admits he's surprised that Harry accepted his invitation to come down for the first time. Harry admits that he's recently been having trouble remembering things and that he's been scared of dying on a bus by himself. MacGyver points out that Harry used to say being scared is worse when he's alone and that now neither one of them is alone. When Harry finds the lab technician's electric razor, he remembers back 25 years ago to when MacGyver's father took Harry's wife to the store during a rainy night.
As Victoria activates the bomb, Phillips finds MacGyver and Harry in the lab. He closes the vault door, trapping them inside, then smashes the locking mechanism. Phillips then rigs two plastic tubes to pump hydrogen sulfide into the vault. Harry smells the gas and MacGyver realizes the danger they're in. MacGyver gets Harry up on a box above the gas line and then tries to rig an electrical current. Phillips reports to Victoria that he's pumped gas into the room but she tells him to be sure they're dead. She tells him she'll wait to set off the bomb until after he reports back. Once Phillips leaves, Victoria kills Fred.
MacGyver rubs rubber tubing on his shirt to generate a current and creates a spark to open the electrical lock. Once outside, he shuts off the gas and they get out of the laboratory and head back down to the lobby. MacGyver has a weakened Harry hide in the women's restroom. Phillips returns to the lab and discovers they've escaped. Once he leaves, MacGyver returns to the lab to get the components for his magnet, then goes back to the lobby door. MacGyver uses the magnet to move the New York lock out of position. Back on the 3rd floor, Phillips hears Harry coughing and captures him.
MacGyver moves the lock out of the way. When it clatters to the floor, the fake guard come to investigate and MacGyver slams the door into his head, knocking him out. After tying him up with a lamp cord, MacGyver heads upstairs. Phillips brings Harry to the lab where Victoria is working on the bomb and ties him up. When Phillips wonders where Fred is, Victoria kills him. She then calls MacGyver on the intercom and informs him that she has Harry and is going to activate the bomb in 15 minutes. Victoria leaves it up to MacGyver whether he leaves the building or searches the place for Harry. Victoria then gags Harry and sets the 15-minute timer on the device.
MacGyver goes back to the computer office and searches the inventory file, but Victoria comes up behind him. She anticipated he would try to access the inventory file and didn't want to risk his disarming the bomb. As MacGyver toys with a ruler, Victoria boasts of her triumphs and MacGyver suggests she let Harry go. When she pulls the trigger, MacGyver jams the hammer with the ruler and knocks the gun aside. Victoria is clearly the superior hand-to-hand fighter and knocks him back into Pete's office. She launches a flying kick and MacGyver ducks out of the way as she goes out the window and falls to her death. MacGyver returns to the computer and as he works, he remembers back 25 years ago to Harry consoling him.
With six minutes remaining, Harry tries to get free. As he looks at the timer, he remembers a state trooper telling him that his wife and son were killed in a car accident. MacGyver, remembering the same thing, discovers that Victoria erased the inventory file. He gets on the intercom and tells Harry to try and send him a signal. Harry chafes the ropes on his feet and pushes himself across the floor on his wheeled chair, while MacGyver checks the backup files only to discover Victoria erased those as well. Harry gets to the phone and manages to tap out "5th floor" in Morse code. MacGyver gets to the lab with a minute and a half remaining, and looks for tools to break the connection between timer and trigger. Nothing he can find will go through the slots on the case and there's a mercury switch set to go off. With twenty seconds remaining, MacGyver takes one of the hockey tickets and inserts them into the slot, jamming the trigger. The timer goes off... and the ticket blocks the connection. Harry takes the last ticket and heads for the hockey game.
The next day, Harry prepares to leave and MacGyver admits he still misses them and Harry agrees. MacGyver packs up and says that he wants to spend some time with his grandpa.