MacGyver is at his apartment working on a new experiment: making non-alcoholic eggnog. His grandfather Harry comes in, but MacGyver has been expecting him: they're going to a hockey game together. They try the eggnog, and Harry isn't too pleased. He notes that it's December 14 on the calendar, and MacGyver has avoided marking it. Harry comments that it's been twenty-five years and MacGyver tells his grandfather he's glad he's there this year.
Evening at the Phoenix Foundation, and Victoria James is parked in the basement garage with three men, one dressed as security guard. They're waiting for a Phoenix worker, Susan Murphy from Demographics, to come out. The men work for a terrorist organization, the Liberation Front, which has hired Victoria to work with them and blow up the building.
As they head out for the hockey game, MacGyver realizes that the tickets he got from Pete Thornton are still at the office. He and Harry drive there to get them.
Victoria approaches Susan as she enters the garage, pretending to be another Phoenix employee. She engages the woman in conversation, recording her name on a hidden digital recorder, then shots her dead. The three men, including Phillips and Fred, hide the body while Victoria gets Susan's key card.
As MacGyver and Harry drive to the Phoenix Foundation, Harry realizes he needs to shave and remembers his wife teasing him when he forgot to shave. MacGyver assures Harry they'll get to the game in time, and remembers back to when he talked to his father about Harry.
As they work, Phillips tells Fred and the disguised security guard that he isn't happy that their superiors have brought in Victoria, an outsider. He points out that she messed up an airport bombing. Victoria, overhearing them, informs them that the Phoenix Foundation stopped her and she's there for revenge. They go to the lobby and knock out the Phoenix security guard. The fake security guard takes his place and they unlock one sealed elevator. Victoria, Phillips, and Fred go up to the 8th floor where the primary lab is. They're unaware that MacGyver and Harry have arrived in the basement.
Victoria and the men get through the security system using Susan's key card and recorded voiceprint. She starts going through the inventory files to locate which lab the explosive device is in. Meanwhile, MacGyver and Harry go to the lobby and the guard casually let them go up. MacGyver wonders why the guard violated security protocols by not asking Harry for an ID. The fake guard unlocks the elevator for them then calls ahead. Victoria has Phillips and Fred hide and then pretends to be a Phoenix employee when MacGyver and Harry arrive. She claims to be Susan Murphy from Demographics, working late to meet a deadline. MacGyver and Harry go into Pete's office while Victoria locates the explosive device. She deletes the record and says goodbye, then tells the fake security guard to seal all elevators and disconnect the outside lines. She then calls her employers with the Liberation Front and informs them that she can kill MacGyver, who has thwarted them in the past. They agree to pay extra and she sends Phillips to dispose of them.
MacGyver finds the hockey tickets and Harry takes them for safekeeping. As he calls him Harry, MacGyver remembers back to when he was a child asking Harry why he preferred "Harry" to "Grandpa" and Harry explaining that "Grandpa" is something to call an old man. MacGyver realizes the elevators are shut down and remembers that Victoria claimed to be with Demographics but was on the 8th floor rather than the 4th. Also, she was wearing lipstick but there wasn't any on the cigarette in the ash tray on the desk. They head for the stairwell and see Phillips coming up. They try and hide but Harry stumbles and gives them away. They run back to 4th and MacGyver rigs the hydraulic hinge on the stairwell door to close slowly. They go down to 3rd and Phillips sees the door closing and starts searching the 4th floor.
Victoria and Fred go to the lab where her explosive device is located. Meanwhile, MacGyver and Harry go down the stairwell to the first floor but discover the fake guard has a put a New York lock on the door. MacGyver heads back to the 3rd floor to get what he needs to make a magnet to bypass it. He tries to call out and discovers the lines are dead. Meanwhile, Phillips finishes his search on the 4th floor and goes down to the ground floor to make sure the New York lock is secure and they couldn't have escaped that way. Satisfied, he starts searching upward again.
Victoria reactivates the bomb while explaining to Fred that she plans to use the device Phoenix captured when her airport bombing failed. That way she can eliminate the evidence, since the bomb bears her unique personal touch.
MacGyver gets to a lab to collect an iron faucet and a battery to make his magnet. He needs copper wiring from a high-security vault. They go in and as MacGyver searches, Harry says that he's usually up on his farm in Minnesota. MacGyver is surprised that Harry came down this year for the first time, and Harry admits that he's been having memory problems recently and was afraid to make the bus trip. MacGyver assures him that it's better to be together to fight the fear. Harry remembers the night 25 years ago when MacGyver's father drove Harry's wife into town.
Victoria finishes reactivating the bomb while Phillips finds MacGyver and Harry in the vault. He closes it, smashes the locking mechanism, and then rigs two tubes to pump hydrogen sulfide inside. Realizing they only have a few minutes, MacGyver gets Harry up off the ground above the gas and tries to rig an electrical current to trigger the lock from the inside.
Phillips meets with Victoria and tells her that he has set up MacGyver's death. Victoria, dissatisfied, tells him to go back and kill them personally. Once he leaves, Victoria kills Fred.
With time running out, MacGyver generates electricity by rubbing a rubber tube on his flannel shirt. The spark opens the electrical lock. They get outside and MacGyver hides the weakened Harry in the women's restroom, figuring Phillips won't look there. MacGyver finishes assembling his makeshift magnet and goes to the lobby. He uses the magnet to shift the New York lock on the other side and then slams the door into the fake guard's face when he comes to investigate.
Phillips hears Harry coughing and captures him, then takes him to Victoria. He ties Harry to a wheeled chair and notices that Fred is gone. Victoria shoots him dead. She then gets on the intercom and tells MacGyver that she has his grandfather and she's activating the bomb with a 15 minute countdown. She figures (accurately) that he won't leave his grandfather. She then gags Harry and activates the device.
With no idea where Harry is located, MacGyver goes back to the 4th floor to locate the inventory files. Victoria, realizing where he would go, arrives and prepares to shoot him. MacGyver jams the hammer of her revolver with a ruler and the two struggle. Victoria's an expert martial artist but MacGyver manages to duck and her flying kick takes her out the window where she falls to her death. MacGyver tries to locate the deleted inventory file and remembers 25 years ago when Harry consoled him.
With six minutes remaining, Harry tries to get free and remembers 25 years ago when a state trooper informed him that his wife and son died when their car went off the road. MacGyver is remembering the same thing, and discovers that Victoria deleted the inventory file and the backup. He calls Harry on the intercom and tries to get him to send a signal. Harry manages to free his feet and pushes himself over to the intercom. He taps out "five" with his feet and MacGyver heads to the lab and finds his grandfather. There's only 90 seconds left on the countdown. The bomb is rigged to explode if it's moved or tampered with. There's ventilation slots but they're too thick for MacGyver to get pliers through to disconnect the timer. With only a few seconds left, MacGyver grabs one of the hockey tickets from Harry, sticks it through the slot, and blocks the trigger from setting off the timer. Harry keeps the last ticket and runs off to catch the last few minutes of the hockey game.
The next day, Harry is preparing to take the bus trip back to Minnesota. The two of them admit they still miss their dead relatives. To Harry's surprise, MacGyver informs him that he's going to go back to the farm with him: he wants to spend time with his grandpa.