In the North Pacific Ocean, the ocean liner S.S. Victoria
is making its way across and First Officer Carole Tanner obtains a weather report from the weatherfax compartment on an approaching hurricane... unaware that there's an explosive charge hidden. She reports to the captain on the bridge, warning that they're heading into the storm. The captain orders a course adjustment and then receives a call from the home office. He tells the other officers they’ve received a bomb threat and goes to the weatherfax compartment to check the report. He arrives there and the bomb goes off, killing him.
At Venice Beach, MacGyver is relaxing with his landlady Suzanne by serving breakfast using a remote control robot. It drops the egg on the floor and MacGyver admits he has to make a few improvements. Pete Thornton calls with a job: someone named Viking is making bomb threats against the S.S. Victoria
and has set off one bomb. MacGyver comes in for a briefing and sees his old friend Charlie Robinson going in. Charlie's wife is pregnant and MacGyver congratulates him, then figures out Charlie's been called in for the same assignment. MacGyver tells him to back off, warning it's not like it was for them in Vietnam and Charlie didn't have a wife and child. Charlie needs the money and insists he's in. Inside, Pete is working with Mike Donahue who is running profiles on suspects. Pete and Charlie come in and MacGyver tries to get Charlie out but Pete notes they worked together as a disposal team in Vietnam. Pete brings them up to speed and explains that the hurricane makes it impossible to put the 1,100 passengers off in lifeboats and Sea & Rescue can't get there in time. MacGyver and Charlie will take a helicopter to the jet, while Pete explains that Donahue, who received a medical discharge in Vietnam, now works with the police and is trying to track down Viking. They get word that the crew has found the bomb hidden in the engine room as an electrical cabinet, below the waterline.
Viking calls in, using a voice scrambler, and knows about Thornton, Donahue, Charlie, and MacGyver. He warns that the bomb is set to go off in ten and a half hours and they need to pay him six million dollars to get him to stop the explosion. He cuts off before they can pinpoint the call and they figure they'll have three and a half hours to work on the bomb. MacGyver and Charlie make the flight to Midway Islands and then take a helicopter to the S.S. Victoria
. MacGyver and Charlie go over their bag of bomb tools and then prepare to cable down. They send down the bag first but the winch malfunctions and the bag and cable plummets into the ocean. With the clock ticking, MacGyver improvises a drop line out of cargo netting and the two men rappel down to the liner. Tanner introduces herself and takes them to the engine room, and explains she hasn't told the passengers what's going on. MacGyver suggests the passengers would want to know.
Acting Captain Tanner takes them to the bomb and removes the cover to reveal a sealed glass panel over a complicated detonation mechanism. There are mechanical and electrical bomb triggers inside the bomb. Tanner puts them in contact with Pete and Donahue, and Donahue recognizes the MO as belonging to an explosives expert, the Ling Cho bomber, they ran up against in Vietnam. There's yellow powder in a dish below a heat sensor but none of them recognize the MO. An officer reports to Tanner that they've found a second bomb and Charlie goes to check it out. Tanner goes on the loudspeaker to inform the passengers of the situation while Charlie confirms the second bomb is identical to the first. There's silicone sealant around the edge of the glass panel. Back in Los Angeles, Viking calls explaining that they don't have the time to stop the bombs and warns that if his instructions aren't carried out and the money delivered, he will disappear. He gives them instructions to deliver the money at a bus depot locker and cuts off. Pete and the others are unaware that it's a pre-recorded call on a timer sent from a hotel room.
Pete authorizes the money drop but Charlie points out that Viking may not tell them how to defuse the bombs even if he gets the money. Charlie goes first and probes the gasket with a dental probe coated in petroleum jelly. He calls off what he's doing and tries to get a sample of the yellow powder. As he penetrates the gasket, air rushes in through the hole. Charlie yells that it's a vacuum as the powder ignites, setting off the heat sensor which triggers the bomb. The crew manage to isolate the leaks and Tanner talks to MacGyver, who is mourning his friend. He talks about how they defused 51 bombs in Vietnam and that Charlie figured it out just before he died. The bomb interior is in a vacuum and the powder is phosphorous. It burst into flame upon contact with air, setting off a thermo couple. MacGyver figures he can fill the vacuum with something else and asks her for neon tubes. They're interrupted when they get word that a third bomb has been discovered. He needs to defuse them in sequence and Tanner volunteers.
At the bus station, Donahue and Pete's men put the money in the locker and stake the place out. Meanwhile, MacGyver prepares to exchange the neon in the tubes for the vacuum inside the bomb. Tanner explains that she became captain by default once the captain died. Pete listens in as MacGyver explains to Tanner how to score the end of the neon tube with a sharpening stone. They break off the tip and immediately plug it with a cork. Then, MacGyver first works the tube through the gasket and pops the cork off the edge of the tray. The gas exchange provides suction, pulling the phosphorus into the tube. He pulls out the tube with the phosphorous and it flashes safely on the outside. Tanner repeats the process and succeeds. With less than an hour remaining, MacGyver notes the thermo couple is German-made and has Pete run the MO against the records. Viking calls Pete and informs him that he has the money, but has decided not to give them the bomb-disarming instructions. Pete calls his men at the bus station, who discover that the locker has a false back and Viking removed the money and escaped. Pete calls MacGyver with the news and warns that it's up to him.
MacGyver proceeds to remove the glass panel and finds four tubes filled with a bubbling liquid. There's a circuit board on the right but as he prepares to examine it, Pete gets a report and calls to tell MacGyver to freeze. The computer says the Ling Cho bomber used an unstable electrolyte fluid. The fluid carries a current and they have to neutralize it. Pete shows the report to Donahue, who doesn't remember it from his time in Vietnam. They figure it's acid, and if they trigger the release it'll short out the trigger and detonate the bomb. MacGyver orders a pastry tube, liquid oven cleaner, and a pint of low-fat milk: injecting the liquids into the acid tubes will neutralize the acid. With nineteen minutes remaining, they inject the neutralizer into the tubes and watch as the neutralizer does its job. MacGyver checks with Donahue, who admits they didn't have much luck doing a post-detonation analysis on the explosion. MacGyver then tells Pete they've got a golf match afterward. Pete calls him privately, having realized MacGyver has never played golf and was giving him a code message. MacGyver tells him to check on the Ling Cho bomber and figure who worked on all of the disarmament teams.
The acid neutralizes and turns clear, and MacGyver and Tanner drain it off. The bombs shut off and everyone cheers in relief. Pete gets the information back on the Ling Cho bomber and calls MacGyver with the information that Donahue worked on all the cases. They're interrupted when the bombs reactivate. MacGyver pries off the bomb casing and finds a 60-second timer with two fuses, yellow and blue. MacGyver calls Donahue and asks him for help, saying he needs help and he's been there. Donahue blurts out blue... and MacGyver pulls the yellow. The bomb deactivates and he quickly tells Tanner to do the same with her bomb. Pete arrests Donahue and MacGyver chats with Tanner afterward. She recommends he stick around for a while and relax... with her.