MacGyver goes to a dockside warehouse to meet with Tan Ye, a Chinese student who takes him inside. A man watching the warehouse calls his boss, Chung Tai Shan. Chung calls him henchman, Li, and tells him to eliminate Tan Ye. Li leaves for the warehouse with his partner Po, unaware that a teenager on a motorcycle is following them.
Tan Ye shows MacGyver crates filled with machine parts and explains that political prisoners in China's notorious "Camp Zero" were forced to make them. The manufactured parts are then falsely labeled and shipped to the U.S. by the Chinese government. Tan Ye has a tape from MacGyver's friend, Mei Jan, that is hidden in the warehouse. As they go to get it, Li and Po arrive outside and the teenager parks out of sight nearby. He goes to a warehouse window and starts taking photos as Chung's men search the place. They find MacGyver, and the photographer throws a garbage can lid as a distraction. MacGyver manages to take on the two men, but Tan Ye is shot and mortally wounded. He tells MacGyver to escape with the tape and leave him. Chung's men corner MacGyver but the photographer rides in and knocks them aside, then tells MacGyver to get on. The two of them burst through a window and escape to safety, while Li and Po discover that the photographer sabotaged their car so they're unable to follow.
MacGyver directs his rescuer to Mei Jan at the hideout where the Chinese students are gathered. The boy introduces himself as Sam and identifies himself as a stringer. MacGyver tells her about Tan Ye's death and gives her the tape. She invites them inside but as they go, Sam opens a locket and intently studies the photo inside.
Li meets with Chung and shows him a phone number they found on Tan Ye's corpse.
As Mei Jan explains Chung's operation, MacGyver decodes the tape and they play the camp footage. Among the prisoners are several students who were arrested at Tianammen Square. Sam explains that he is on the trail of Chung, a former Colonel in the Red Chinese Army ten years ago. Chung killed Sam's mother, a photojournalist, when she was working on a story on the dissident movement. Sam watched from hiding as Chung gunned his mother down "resisting arrest." MacGyver admits he was involved with a female photojournalist who died ten years ago in China, and Sam explains that his mother was Kate Malloy. Kate is MacGyver's old girlfriend and Sam shows him the locket. Inside is a photo of his mother and the man she said was Sam's father: MacGyver.
The next day, they go to the docks and discover Pete is there with the police. Chung has already removed all evidence of the crates from the warehouse, as well as Tan Ye's body. As they go in, MacGyver explains to Pete that Sam is his son. Inside they find a dead beetle and Sam and MacGyver both realize an entomologist can identify where in China it came from. Sam also figures they can use the machine part MacGyver kept to identify the metal's geographic source via spectrography. MacGyver admits to his friend that he's not sure if he's ready to be a father, but Pete tells him he's always been good at adapting.
Back at MacGyver's apartment, Sam explains that after his mother's death, he hiked out of China on his own then made it to the state where Kate's relatives took him in. He never knew his father's name and only had a photo to identify him. Kate never told Sam who his father was, and said he was busy traveling the world helping people. She'd planned to introduce them when Sam was older.
Chung confirms that MacGyver works with the Phoenix Foundation and Mei Jan. If Mei Jan turns the tape over to the U.S. government, it will disrupt the current round of trade talks. He tells his men to trace the phone number they found on Tan Ye's body.
As Sam and MacGyver eat, Sam explains that his real name is Sean Angus Malloy, but he uses "Sam" for short. Pete calls to confirm they've pinpoint the location of Camp Zero from the beetle and the metal parts. He plans to go to the State Department with the evidence but warns they don't have anything to connect it to Chung. When Pete mentions Chung's address, Sam slips away. MacGyver discovers he's gone and goes downstairs to find him packing a gun. Sam says that he plans to kill Chung in the name of justice, but MacGyver insists that they have to be better than Chung and a gun isn't the answer. Sam hands the gun over and the two embrace.
Sam and MacGyver go back to the dissident's lair to take Mei Jan to the State Department. Li and his men ambush them and abduct Mei Jan. they take her to the dock where Chung is preparing to leave the country on his freighter. They lock her in a cabin with Tan Ye's corpse and prepare to set sail. Once out at sea, they'll drop all evidence of the labor camp goods… and Mei Jan as well.
Pete tells MacGyver and Sam that Chung has filed departure papers. MacGyver prepares to go after his friend and Sam insists on coming along. They get to the docks and slip on to the freighter via a cargo pallet. They spot Li guarding Mei Jan's cabin and Sam distracts him while MacGyver knocks him out. Sam drags Li into hiding and notices his gun, then takes it for himself. MacGyver frees Mei Jan and she tells him the evidence is in the main hold. Sam goes after Chung and Po spots him. MacGyver sees Po preparing to shoot and yells, drawing his attention. Po shoots MacGyver and the impact knocks him into the cargo hold where he crashes onto some crates. Chung's men arrive and quickly capture Sam and Mei Jan.
Chung's men lock Sam in the hold with MacGyver and take Mei Jan to the bridge. Chung tells her that she's accomplished nothing and destroys the tape, and promises that she'll be going to Camp Zero.
As Sam tries to find a way to escape, he talks about sprouting wings. MacGyver runs with the idea and notices a high-pressure deck washer. He builds harnesses out of discarded valve wheels, then hooks up the washer to spray handles with PVC piping and attaches the handles to the harnesses. He and Sam then activate the water, which provides enough pressure to push them up and out of the hold. They head for the bridge and MacGyver has Sam open up a flare gun shell. They dump the powder into the bridge via a ventilation pipe and ignite it. Mei Jan grabs a gun and runs out along with the men. On the deck, Chung prepares to shoot MacGyver but Mei Jan gets the drop on him. She prepares to shoot him as revenge for Tan Ye. However, Sam convinces her to drop the gun and let Chung face legal justice, just as MacGyver said earlier. MacGyver says that Kate would have been proud of her son.
MacGyver and Sam are packing for a trip when Pete arrives. He has a new contract for MacGyver, but MacGyver says that he has some catching up to do and he and Sam are hitting the road. MacGyver and Pete exchange goodbyes and Sam promises to take care of his father, and then father and son ride off toward the horizon.