MacGyver follows Dave Edwards, a computer engineer working for a Phoenix subcontractor. A check has shown up that Edwards has too much money and is selling secrets. MacGyver is unaware that Papillon, Edwards' employer, is has spotted him. MacGyver trails Edwards to a bar and Papillon tells his assistant Herrill to have their man Kreese sends Edwards to the secondary drop while Herrill disposes of MacGyver. MacGyver goes up to the bar near Edwards, and Kreese signals Edwards. When MacGyver goes after Edwards, Herrill and Kreese cut him off. MacGyver jumps behind the bar and pours dishwasher powder on the bar top, then uses an air hose to spray it in the faces of his assailants.
Outside, Papillon confronts Edwards, pulls a gun, and demands the "butterfly." Edwards tries to run but Papillon shoots him down. MacGyver comes out and spots an envelope in Edwards' hand. Inside is a butterfly in a plastic bag.
Later at the Foundation, Pete discovers that the butterfly wing conceals a microdot. The information is the schematics for the Rains satellite linking system, which are useless without the schematics from the other three companies. MacGyver figures that whoever is responsible may have already obtained the other schematics. Pete promises he'll notify Colonel Collins but warns that he can't tell MacGyver everything because the government project is on a need-to-know basis. Pete's son Michael, working at the Foundation, drops off some reports nd jokes with his father. After he goes, MacGyver is happy that Pete's getting along with his son after Pete put Michael to work there.
Papillon meets with Chaz Gordon, one of Dave's friends and fellow operatives, and exchange the proper passwords. Papillon lies and claims that Dave was shot by a government operative and Chaz now has to run the operation. Papillon assures him that his time has come to take charge and get the final set of schematics.
Pete meets with Collins and explains what has happened. MacGyver wants to know what the Rains system involves and Collins insists it's top secret. MacGyver refuses to back down and quits, and Collins reluctantly gives in. He explains Rains is a radar disruption satellite system. Collins and Pete take MacGyver to the high-security assembly room and Pete assures Collins that only he and the head scientist have the access card. They go in and Collins explains that a hostile country is preparing a biological weapon and they need the Rains unit to send in a surveillance jet and get evidence to take to the UN.
At a health club, Chaz meets with Simon and Alex, two of the five members of their circle. Chaz assures them that their fifth member will get the final schematic: Michael Thornton.
At the Foundation, Pete drops in on Michael and MacGyver as they try to descramble Edwards' personnel file, which was sabotaged with a virus. MacGyver is checking on Edwards' college records.
At the health club, Chaz gives Michael a camera to take photos of the schematics. Michael warns it won't be that easy but they provide him with a device that will copy magnetic code strips. They tell him to get the card from his father.
Later, MacGyver has discovered that the same person who infected Edwards' employee records also struck at his college information. Pete mentions books and MacGyver calls the state university library. As Pete leaves, Michael approaches him and they go into Pete's office. Michael gives him a new cashmere jacket as a present and overrides Pete's objections. As Pete goes to the mirror to check the fit, Michael takes his key card, scans it, and returns it to Pete's pocket. Pete talks about how he was never at home enough to be a husband or father, and offers to try and be friends.
Later, MacGyver comes in and asks if Pete has seen Michael. He then reveals that Edwards set up the campus computer club and five club members work with companies involved in the Rains project. Michael is one of the five. Pete insists it's impossible and says that Michael just gave him the jacket. MacGyver realizes that Michael was alone with Pete's jacket with the key card on it.
Michael uses the duplicate key to enter the Rains assembly chamber and takes photos of the schematics. However, Collins, Pete, and MacGyver arrive to confront him. Michael admits that at first it was about money and he's angry that they killed Edwards. When MacGyver insists that Edwards' contact killed him, Michael blurts out Papillon's name. MacGyver suggests they give Papillon what he wants... in person, using Michael as bait. Collins offers Michael a deal but Pete refuses, insisting that Michael do it because he wants to do the right thing. Michael agrees to help and Pete admits he doesn't understand how Michael lost the ability to determine right from wrong. Michael points out that Pete used to say that his job involved the gray area and Pete insists that he worked within the law for his country. He leaves his son, alone.
That night, a wired Michael meets with Chaz and demands more money for the schematics. Outside, Pete, MacGyver, and Collins listen from a surveillance van. Michael offers Chaz a cut, insisting they're taking all the risks. He offers to meet with Papillon and Chaz agrees. Michael sets up a rendezvous at a shopping mall the next day.
The next day, Chaz goes to Papillon's country house and tells him about Michael's demands. Papillon tells Chaz that he's giving in but sends Kreese to impersonate him, since Michael has never met Papillon. Herrill will accompany Chaz and bring him and Michael back. Once Chaz is gone, Papillon gives Kreese a prussic acid sprayer and orders to dispose of Chaz and Michael once Herrill has the schematics. As he demonstrates it, Kreese jumps back, startled, and knocks over one of Papillon's cases of butterflies. He also gives Kreese a dose of the antidote to be safe. As Kreese leaves, he steps on the broken butterfly display case.
At the mall, Pete is working undercover at a food kiosk as Collins and MacGyver prepare Michael at a closed store. Michael claims the whole thing was just a game but MacGyver points out he hurt Pete and that Pete loved his son even though he wasn't there. Collins sends Michael out to meet with Chaz. Chaz points out Kreese and claims he's Papillon. Kreese moves in and Pete spots the acid sprayer. He runs over and tackles Kreese and gets a faceful of prussic acid. Herrill pulls a gun and takes Michael away, while Kreese takes the antidote and then collapses, dead. Collins and MacGyver come over, smell the prussic acid, and realized what happened. With less than two minutes left, MacGyver goes to a nearby photo store and gets some photo fixer, which contains sodium thiosulfate, and has Pete drink it.
At Papillon's house, Papillon takes the photos of the schematics and Chaz realizes that his superior will dispose of him and Michael. Papillon goes to develop the film while Herrill watches them.
At the mall, MacGyver and Collins realize that Papillon gave Kreese disguised cyanide to tie up a loose end. MacGyver spots a label from the butterfly case on Kreese's shoe. They figure Papillon is a butterfly collector and Collins traces magazine subscribers cross-referenced with the DSX files.
Papillon confirms the photos are legitimate and orders Herrill to take Michael and Chaz out and have them dig their own graves.
Collins matches the magazines to Papillon's real name, and his identity as a former naval attaché suspected of espionage. They have his address but Collins can't go in without a search warrant. Pete insists on going to rescue his son.
Papillon and Herrill take Michael and Chaz to the lake near a chopper pad. Pete and MacGyver arrive and split up. The helicopter with Papillon's buyer arrives. MacGyver gets to the helipad controls and changes the landing lights to warn them away. Papillon goes to investigate while MacGyver rewires the control box. Herrill prepares to shoot Michael and Chaz but Pete arrives and forces Herrill to drop his gun. Chaz tries to run and Herrill struggles with Pete. Michael comes to his father's aid and is shot in the leg before Pete can recover his gun and stop him.
Papillon gets to the control panel and it shorts out, startling him. MacGyver jumps out of a tree to tackle him and knocks him unconscious. Papillon's buyers, nervous, fly away.
Later, MacGyver comes to see Pete and try to console him, noting parents can only do so much. Pete isn't convinced and wonders what he's been doing wrong. Michael arrives, on crutches, and explains that thanks to his cooperation, he'll get a reduced sentence but still serve time. He admits that he's scared and Pete insists that he's still his friend no matter what.