MacGyver is following Dave Edwards, a computer engineer employed by one of the Phoenix Foundation's subcontractors. Edwards' finances show that someone is paying him for illegal activities. MacGyver follows Edwards to a bar while Edwards' boss, Papillon, watches them both as they go inside. Papillon tells his henchman Herrill to send his other man Kreese inside to get Edwards out, while Herrill kills MacGyver. Herrill goes inside and signals Kreese, who gets Edwards out of the bar. Both men close in on MacGyver, who blinds them with dishwashing powder spread across the bar top. Outside, Papillon meets Edwards and asks for a butterfly. Edwards tries to run and Papillon kills him. He's forced to leave when MacGyver arrives. MacGyver searches Edwards' body and finds an envelope containing a butterfly.
At the Foundation, Pete examines the butterfly and discovers a microdot on its wing. The microdot contains the schematics for one quarter of the RAINS satellite linking system. However, the schematic is useless without the other three quarters. MacGyver suggests they check with the other subcontractors to see if any information has been smuggled out. He asks for more information on the project but Pete explains that Colonel Collins, their government liaison, has restricted the data to need-to-know. Pete's son Michael drops off some reports and Pete admits that he's proud to have his son working there.
At a health club, Papillon meets with Chaz Gordon, a friend of Edwards. Papillon claims that the government shot Edwards and informs Chaz that now he has to run the operation and get the final set of schematics.
Pete briefs Colonel Collins on what has happened. MacGyver demands answers and Collins refuses to reveal anything until MacGyver threatens to quit. Collins takes MacGyver and Pete to a high-security vault in the foundation's basement where the unit is being assembled, and informs MacGyver that RAINS is a radar disruption satellite system that allows planes to avoid enemy radar. As Pete lets them in using his passcard, Collins explains that the U.S. is sending a surveillance jet into enemy territory to confirm the presence of a biological weapons plant. They need the RAINS unit to get the jet in undetected and get the necessary information to present to the UN.
At the health club, Chaz meets with Alex and Simon, two more of the five friends working for Papillon. They're concerned they can't get the final schematic but Chaz greets the fifth friend, the one who can get the info: Michael Thornton.
MacGyver goes to work trying to read Edwards' corporate personnel file. Someone has used a virus to wipe the file so MacGyver checks Edwards' college file. Meanwhile, Chaz gives Michael a camera to take photos and a device that will copy passcards. When Michael notes that only two people at the Foundation have a passcard, Chaz tells him to Pete's.
MacGyver discovers that the same virus was used to corrupt Edwards' college files. Pete gives him the idea to check the physical records at the university library. MacGyver leaves and Michael arrives with an expensive new cashmere jacket for Pete. He convinces his father to try it on and then takes his passcard and scans it when Pete is in the next room. Pete comes back and admits that he'd like a chance to at least be friends and make up for all the years he was absent.
Later, MacGyver returns and asks Pete if Michael was there. He explains that Edwards' files show that he set up the campus computer club. Five of its members now work for the companies involved with the RAINS system, including Michael. Pete doesn't believe it and notes that Michael just gave him the jacket as a gift. MacGyver spots Pete's passcard and figures that when Michael was alone with Pete's original jacket, he took the keycard.
Michael enters the RAINS assembly chamber using the duplicated passcard. He takes photos but MacGyver, Pete, and Collins arrive to capture him. Collins interrogates Michael, who admits that it wasn't just the money but getting revenge for Edwards' Death. MacGyver figures that Edwards' contact killed him, and Michael blurts out Papillon's name. MacGyver suggests they use Michael to set a trap and Collins offers Pete's son a deal. Pete insists that Michael has to do it because it's the right thing, not because he gets a deal out of it. Michael agrees to help them and Pete wonders how things went wrong. Michael insists that he's doing the same thing Pete used to do, working in the gray areas of the law. Pete defends himself, insisting that he worked within the law and for the sake of his country, and then sadly walks away.
That night, Michael meets with Chaz and tells him he wants more money. MacGyver and the others are in a nearby van listening in on a hidden transmitter. Michael offers to cut Chaz in on the extra money he makes and says they deserve it for their efforts. Chaz is reluctant to relay the message and Michael insists on meeting Papillon personally at a shopping mall the next day.
Chaz goes to see Papillon at his country estate and tell him about Michael's demands. Papillon comes up with a plan and tells Chaz that since Michael has never met Papillon, Kreese will impersonate him from a distance. Herrill will escort Chaz and Michael back to the estate. However, once Chaz Leaves, Papillon gives Kreese a prussic acid sprayer and tells him to kill Chaz and Michael once Michael has turned over the schematics. When Papillon demonstrated how to load the device, Kreese flinches and knocks over one of Papillon's rare butterfly cases. Papillon gives Kreese an antidote capsule to be on the safe side. As Kreese leaves, he steps on the shattered case.
Pete is working undercover as a vendor at the mall while Collins and MacGyver set up in a closed store. They wire Michael and MacGyver wonders how he could have hurt Pete. Michael claims it was just a game to him but MacGyver insists that Pete loved him even if he couldn't always be there.
Michael goes out to meet Chaz, who points out Kreese and claims he's Papillon. Kreese comes over and Pete spots the acid sprayer. He tackles Papillon's henchman and gets a faceful of the prussic acid. Kreese takes the antidote and then immediately collapses, while Herrill gets Michael and Chaz away at gunpoint. MacGyver and Collins run over and Collins realizes that Pete has been sprayed with prussic acid. Pete has only two minutes to live, and the only antidote is sodium thiosulfate. MacGyver goes to a nearby photo shop and borrows some photo fixer, which contains sodium thiosulfate, and then mixes it with water and has Pete drink it.
Herrill take Chaz and Michael to Papillon's estate. Papillon takes the camera with the schematics and prepares to dispose of both of them once he confirms the schematics are real.
At the mall, MacGyver and Collins figure that Papillon gave Kreese poison claiming it was an antidote so he could dispose of a loose end. MacGyver spots the label from the butterfly case on Kreese's shoe and concludes that Papillon is a butterfly collector. He has Collins do a match of DSX files to butterfly magazine subscriptions.
Papillon confirms the schematics are real and orders Herrill to take Chaz and Michael out and kill them.
Collins gets a match with one suspected espionage agent: Roger Sanborn, a former naval attaché who quit when he was accused of espionage. Collins gets Sanborn's address but can't do anything without a search warrant. Pete insists on going to rescue his son and MacGyver accompanies him.
Papillon and Herrill take Chaz and Michael to the nearby lake. A helicopter pad is nearby. MacGyver and Pete arrive and split up to rescue Michael. Papillon's buyer arrives by helicopter and prepares to land, but MacGyver gets to the light control and signals them away. He rewires the control box, while Papillon realizes something is wrong and goes to investigate. Pete manages to surprise Herrill and force him to drop his gun. However, when Chaz tries to run, he distracts Pete and Herrill attacks him. Michael tries to help and Herrill shoots him in the leg before Pete can disarm him.
Papillon tries to activate the proper lights and MacGyver's rewiring job shocks him. MacGyver tackles him and knocks him unconscious, while Papillon's buyer flies away.
Later, MacGyver visits Pete as he waits for Michael to return from his hearing. Pete worries that he hasn't done enough and MacGyver assures him that there's only so much that parents can do. Michael arrives to inform them that he's getting a reduced sentence due to his cooperation. He admits to Pete that he's scared and his father assures him he'll be there as his friend no matter what.