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A distraught, soaking wet man stumbles through Boston's Chinatown, looking for an address. He is buzzed up into an apartment and asks his host, Dr. Min Chae, if the others have arrived. When he is told he is the first to arrive, he believes these others to be dead. Chae leads him to a room with many beds set up in it and has him lie down. He starts complaining of stomach pains, and Chae puts on a pair of rubber gloves and cuts the man's shirt away. A shape seems to be crawling up his stomach beneath his skin and Chae watches as a creature with writing tendrils crawls out of the man's mouth.
Peter and Walter Bishop meet Agent Olivia Dunham at the Dorchester Bay Inlet in Boston. Agent Philip Broyles tells them that a Chinese merchant ship caught fire and sank in the inlet. Nearly 30 bodies have washed up on shore, all of which have the tendriled creatures pouring out of their mouths. When asked if he's ever seen anything like it, Walter says that it is similar to a parasite found in China, but that he had never seen one of such size nor in humans. A survivor is found in the water and Walter has her rushed to the hospital to see if they can remove the parasite in time to save her.
At the hospital, Dunham and Peter meet with the survivor, Mae Lin. It appears that she escaped infection. She tells them that her fellow travelers came from China looking for work. Aboard the ship, they were all given what they were told was medicine for sea sickness. However, Mae Lin did not take it because her father was a fisherman and she is used to boats. Dunham and Peter assume that the medicine is what caused the infection. Mae Lin tells them that there is a second boat on its way to Boston and that her husband and daughter are on it.
In Chinatown, Chae welcomes another soaking wet refugee from the merchant ship, telling him he is the first to arrive. However, in the apartment there are several dead bodies draped across the beds. Chae is putting the parasites in a vat of boiling liquid. He appears to be harvesting something resembling eggs from the parasites. He puts a pile of white powder into an envelope.
Agent Broyles has arrested a man in connection with the sunken ship. Agent Dunham and Peter arrive to question him, but Peter looks at the man's tattoos and determines that he is a Triad gangster and will not talk. Dunham explains that his gang ships heroin, not people, but Peter says that some parasites have been known to excrete opiates. As the three discuss the possibilities, the man sneaks a razor blade out of his mouth, slashes his own throat and dies smiling.
In the Harvard lab, Walter and Agent Astrid Farnsworth are dissecting the parasites. He agrees with Peter and Dunham's assumption that the parasite larvae was put in the sea sickness capsules, causing Peter to remark that the Chinese nationals were "human incubators" for these creatures. Walter holds the live parasite while Astrid takes a sample to test for narcotics. Suddenly, the creature wraps itself around Walter's arm and bites into him, beginning to feed. While Walter remarks that the initial bite was quite painful, he says that the experience is pleasant -- clearly stoned. Astrid struggles to pull the creature off of Walter, leaving him in a daze.
Agent Broyles tells Agent Dunham and Peter that a John Soo is the suspected head of the Triad gang. They follow up on a lead, interviewing Elizabeth Jarvis, a woman who invested in a Soo shell company. While Dunham interviews the woman, Peter looks around her home, noticing a complete lack of dust and that the windows are hermetically sealed. Upon his return to the lab, he asks Walter what the connection could be between the parasites and an obsessive-compulsive germaphobe. Walter has a theory: ever since the parasite infected him, his white blood cell count is up, he has developed new anti-bodies and even his gas from earlier is gone.
He surmises that the parasite is not a narcotic, but a medicine. Walter says that the parasite was engineered specifically to grow in people and develop this medicine. He says that the key is its lymph gland, which is what Min Chae was harvesting earlier. Agent Dunham and Peter return to the Jarvis home to interview Matt Jarvis, Elizabeth Jarvis' son. Peter assumes that Elizabeth is sick and that is why she partnered with the Triad. However, he learns that it is actually Matt who needs the treatments. His body does not produce enough white blood cells to fight infection, so he receives monthly treatments.
Walter makes plans to visit several herbalists in Chinatown to see if he can find a match for their parasite. In Chinatown, Walter catches Astrid following him and expresses his disdain at constantly having people supervising him. The two then visit the next herbalist on Walter's list - Min Chae. Walter lets it slip that they have seen the parasite. Chae places a call to another gang member, who follows the pair. On the street, Astrid buys drinks for her and Walter, but when she turns around, Walter is gone. Astrid calls Peter in a panic, but the two assume that Walter has stalked off on his own as a display of independence. Astrid returns to the lab to see if Walter is there, but finds two Triad gangster instead, attempting to steal the parasite.
Agent Dunham and Peter return to the lab to find a beaten, bloodied and unconscious Astrid Farnsworth on the floor. When she comes to, she tells them that two Triad members took the parasite. As Dunham tends to Astrid, Peter receives a call from Chinatown: someone has found Walter, lost on the streets. He heads to Chinatown to pick him up. Walter tells Peter that he mentioned their parasite at one of the herbalists; Peter realizes that that must be the reason why Astrid was followed. Meanwhile, Dunham has grilled Elizabeth Jarvis and has gotten the information on the second boat. The FBI raids the ship but they are too late: the hosts are gone.
Peter and Walter spy the hosts being led into Chae's apartment above the herbalist shop. He calls Dunham for back-up, tells Walter to stay in the car and then heads into the building. He sees Chae about to operate on one of the Chinese nationals. He stops Chae, but is attacked by other Triad gang members. They tie Peter up and feed him one of the worms. The FBI bursts in and Dunham shoots Chae. Peter is able to spit the worm out before swallowing it. The FBI transports the Chinese nationals back to the hospital, where Broyles tells Dunham and Peter that they will all be fine. He also reveals that John Soo is not a real person, but a front for Min Chae and his operation. Dunham visits Mae Lin and her family in the hospital room, returning a toy to her daughter that she had left on the boat.
Walter wakes Peter up back at their apartment. He tells him that while he is on the road to becoming independent, he will occasionally still get lost and will need Peter to find him. As the episode ends, Walter reveals that he has implanted a tracking device into his own neck to make it easier for Peter to find him next time. Peter can only smile as he looks at the transponder his father gives him.