The S.S. Victoria is crossing the North Pacific, and First Officer Carole Tanner receives a weatherfax that there's a hurricane coming their way. She's unaware that there's a bomb hidden in the weatherfax compartment. She gives the captain the weather report, and he orders them to change course to avoid the storm front. The home office calls and informs the captain that there's been a bomb threat. He goes to check the weatherfax compartment, and the concealed bomb goes off.
MacGyver is home at Venice Beach entertaining his landlady Suzanne with a robot that serves breakfast. It has problems handling eggs and makes a mess. As he cleans up, MacGyver gets a call from Pete Thornton: an extortionist calling himself "Viking" has made a bomb threat and set off one bomb aboard the S.S. Victoria. Pete wants MacGyver to help out, and promises him a surprise. MacGyver arrives at headquarters to find his old pal Charlie Robinson just going in. They served together in Vietnam as bomb disposal experts, and now Charlie is married with a child on the way. However, MacGyver quickly realizes Pete has called Charlie in on the same assignment. He tells Charlie to refuse the mission but Charlie needs the money.
At headquarters, Pete is working with Mike Donahue, a former Vietnam officer who worked in bomb disarmament and is helping them try to get a handle on Viking. Pete explains that they can't evacuate the S.S. Victoria because the hurricane makes it impossible for the passengers to put to sea in lifeboats, and they're too far away for evacuation helicopters to arrive. MacGyver and Charlie will take a jet to Midway and then a helicopter to the liner. Donahue, who works with the police, will help Pete and his people try to put together a profile on Viking. The crew informs them that they have located the bomb in the engine room, hidden behind a fake electrical panel.
Viking calls headquarters, and reveals he knows about all of them, addressing them by name. He tells them they have ten and a half hours to pay him six million dollars to stop the detonation. They're unable to pinpoint the call and MacGyver and Charlie quickly depart. Their helicopter arrives above the liner but the winch malfunctions as they lower their bomb disarmament equipment to the deck. MacGyver unravels a cargo net and uses it a rappel line so he and Charlie can descend to the liner. Tanner, now the Acting Captain, introduces herself and takes them to the engine room. En route, she tells them that they haven't informed the passengers about the bomb, but MacGyver notes that he'd want to know if his life was in danger.
They examine the bomb, which is a large mechanism with a glass front. The bomb is covered with triggers and they radio in the description to Donahue. He recognizes it as the work of the Ling Cho Bomber from Vietnam, who was never caught. However, the primary trigger in the bomb is a dish of yellow powder with a heat sensor nearby, which doesn't match with any known MO. Tanner gets word that there's a second bomb hidden elsewhere in the ship. Charlie goes to investigate it while Tanner decides to inform the passengers what's going on. The two bombs are identical, and Charlie notes that there is a silicone sealant around the edge of the glass panel.
Viking calls headquarters to give them instructions to deliver the money, warning that if they don't deliver in time and in good faith then he'll disappear for good, leaving the bomb to detonate. He gives them instructions to deliver the money to a locker at a bus depot and hangs up. Pete and the others are unaware that it's a pre-recorded call on an automatic dialer.
Pete agrees to pay off Viking but Charlie and MacGyver figure that Viking will take the money and let the bombs explode. Charlie insists on going first to examine the bomb. He and MacGyver are in constant contact via radio and he talks his way through the process: first he takes a dental probe, coats it with petroleum jelly, and slips it through the silicone sealant holding the glass in place. He prepares to touch the probe to the powder to get a sample, but air starts to hiss through the ruptured seal. Charlie yells out that it's a vacuum… and then the powder ignites and the bomb detonates.
The crew manage to contain the resulting leak and Tanner checks on MacGyver, who is mourning. MacGyver talks about how together he and Charlie defused 51 bombs in Vietnam and if they disarm this bomb, it's because Charlie figured out in his last seconds. The inside of the bomb is a vacuum, and the air set off the yellow powder: phosphorous. The heat sensor set off the bomb. Tanner wonders what they can do and MacGyver says that they'll need neon tubes. However, Tanner gets word that the crew have discovered a third bomb. MacGyver needs someone to defuse it and Tanner volunteers.
Pete's men take the payoff to the bus depot and leave it in the indicated locker, then settle in to watch the place. Meanwhile, MacGyver goes to work, taking a neon tube from the ship's bar. Tanner follows the same procedure as he breaks off the end of one tube and then quickly blocks it with a cork. He then pushes the tube through the gasket, scrapes the cork off the edge of the powder dish, and the resulting gas exchange sucks the phosphorous into the tube. MacGyver pulls out the tube and the phosphorous harmlessly ignites. Tanner repeats the process and defuses the trigger on her bomb. MacGyver gives Peter a description of the heat sensor and has him check the records.
Viking calls headquarters and informs them that he has the money. However, since they tried to capture him at the bus depot, he refuses to give them the disarmament instructions. Donahue and Pete's men check the locker and discover that Viking extracted the money through a panel in the back and escaped.
MacGyver and Tanner get inside their respective bombs and find four tubes filled with a bubbling liquid, attached to a circuit board. MacGyver prepares to drain off the fluid but Pete tells him that they've turned up a match with the Ling Cho Bomber, who used acid as a trigger. The acid carries a current and it's broken, the bomb goes off. However, if the acid spills out then it will short out the circuit and trigger the bomb. MacGyver has the crew provide him with a pastry tube, low-fat milk, and liquid oven cleaner. He and Tanner mix the liquids together and then inject it into the tubes. The liquid neutralizes the acid: all they have to do is wait for the chemical reaction to take place. As they wait, MacGyver talks to Donahue who says they never got a handle on the Ling Cho Bomber. MacGyver tells Pete they'll play golf when he returns. Knowing MacGyver doesn't play golf, Pete contacts him privately on the radio and MacGyver says that the triggers must add up to a single artistic MO. He asks Pete to see who worked on all of the disarmament teams in Vietnam.
The acid turns clear, neutralized, and MacGyver and Tanner safely drain it off. The bombs shut off and Pete contacts MacGyver privately to tell him that Donahue worked on all the Ling Cho cases. They're interrupted when the bombs reactivated. MacGyver and Tanner yank off the covers to reveal a sixty-second time and two fuses, blue and yellow. MacGyver admits he can't figure it out and Donahue for his advice. Donahue tells him to pull the blue fuse… and MacGyver tells Tanner to stop. He pulls the yellow fuse, stopping the countdown. He quickly tells Tanner to do the same, and she defuses her bomb. Pete arrests Donahue, while Tanner suggests that MacGyver stay on the liner for a while and relax with her.