House implores Cuddy to let him take a sample from Joe's brain. She refuses because Joe's death made this a bio-safety hazard. The CDC will perform the autopsy and return results to them in three days. House points out that Foreman might be dead in 36 hours, but Cuddy doesn't budge. They don't have the tools to do this safely, so it's out of her hands.
House comes up with an idea, and he heads down to the isolation room. He slides an ice pick and hammer through the airlock, telling Foreman to cut into Joe's eye in order to extract some brain tissue. Cuddy rushes down and orders Foreman to stop. She then has another doctor suit up and enter the room to restrain Foreman. House presses Foreman to continue. Instead of slamming the pick into Joe's eye, Foreman drives it into the mattress. Foreman senses that it didn't feel right, but he removes a sample from the mattress anyway thinking that it is Joe's brain. Realizing that Foreman has Anton's Blindness, House asks Cuddy if she still wants to wait for the CDC.
House, Cameron and Chase convene for a differential diagnosis on Foreman. They throw out various diseases, none seeming likely to be the culprit. House orders them to start treatment for everything they can think of. He leaves to find another brain to biopsy. Even though they are worried that a heavy regimen will trash Foreman's organs, Chase and Cameron slide the pills to him. Foreman feels each pill and discerns what it is for. He realizes that they have no idea what's afflicting him and grudgingly takes the medication.
House goes to Joe's apartment in a biosuit. He has the rat that he trapped in Stacy's attic months ago with him. He calls Foreman in the iso room and asks him to detail his steps. House carefully inspects each area, making sure to expose the rat to everything that Foreman was around. When House hangs up, Foreman calls his father.
The next morning, Wilson finds House staring intently at his computer. House has set up a webcam to monitor the rat in his own kitchen. As soon as the rat becomes sick, House will perform an autopsy.
Cameron draws blood from Foreman and he notices that she left the tourniquet on his bed. His vision is returning in response to the treatment. Yet which treatment worked? House wants to stop individual medicines one by one to find the one that caused a regression in his vision. Before Cameron can do anything, Chase reports that Foreman's amylase and lipase levels are three times the normal level. His pancreas is failing due to the meds, which must be stopped immediately.
House goes to Foreman and tells him what's happening with the meds. Foreman asks him to lower the dosages, but even lower doses would be toxic. If they continue the meds, Foreman will appear to see for the next four hours until he dies. If they stop, he'll lose his vision but buy time for a diagnosis. Foreman agrees to cut the meds.
Foreman's father Rodney arrives, and House explains to him that a brain is available but Cuddy won't allow them to autopsy it. House then escorts Rodney to Cuddy's office, and the man questions her about her decision. Cuddy struggles to give him an answer, and explains that the deadly infection Foreman has could put many more lives in danger. This Rodney understands.
Foreman assures his father that it won't be a painful demise. Wilson catches up with House outside of the morgue to report that the rat is still healthy. He also has noted that House is preoccupied with the guard stationed in front of the cooler holding Joe's body.
Foreman's vision regresses and he has reached an eight on the pain scale. The disease is progressing faster than it did in Joe. House is slightly encouraged by the anomaly and asks the team what that could mean. Cameron comes up with the fact that many diseases affect blacks differently than whites. House has them look up all bacterials, fungals, toxins and parasites to find any documented racial disparities. House remembers that the rat is still perfectly healthy and he thinks perhaps that's the difference between Foreman and Joe.
Cuddy visits Foreman in isolation. He's enraged that she won't ignore CDC policy to help save his life. House comes in and announces to Foreman that he's dying too fast. He holds up a vial holding legionella pneumophila. Joe had Legionnaire's disease when he got infected, and it somehow slowed down the progression. Joe didn't die until they cured the Legionnaire's. Foreman refuses to inject himself. House simply opens the door to the isolation chamber and tosses the vial in. It shatters.
Cameron watches as Foreman takes his own temperature. It's down to 101.0, and Foreman reluctantly admits that his pain is no worse. He did contract Legionnaire's, and it has indeed slowed the progression of the mystery disease.
With the rat still not sick, Wilson wonders aloud what House will do if the rat never falls ill. House has a realization, and declares Wilson's suggestion as brilliant. He walks out and asks Cameron what illnesses affect humans and not rats. House then tells her that she didn't become sick because whatever it is isn't blood-borne.
Chase suggests that some bacterial infections don't affect rats, but Cameron counters that Foreman has tested negative for every bacterial infection that affects the brains. House observes that when they test for bacterial infections, they're really looking for antibodies. The body might not be fighting the infection. If the body doesn't recognize the first infection, that infection will run rampant through the body. Yet when Legionnaire's is contracted, the body does recognize that and increases white cell count to stave it off. The body unintentionally fights the first infection as well. They need to figure out what bacterial infection affects humans and not rats which the body is unlikely to recognize.
House informs Foreman that the answer is Listeria, so he will start him on Amp and Gent. He puts the antibiotics in the airlock, but Foreman requests certainty. He asks House to perform a white matter biopsy. House refuses, because any slip will render Foreman an invalid. Foreman fears the antibiotics will bring back the pain if House is wrong. House begs him to try the medicine first. If it doesn't work, he will biopsy the brain again. Foreman takes the pills.
As Cameron changes the antibiotics IV bag, Foreman writhes in pain. He implores her to put him in a coma, asking her to be his medical proxy. He quotes from her medical journal article about the importance of a well-informed decision. Foreman then apologizes for stealing her material for his own article. She agrees to be his proxy, but doesn't forgive him for what he's done.
Chase finds Rodney Foreman in the hospital chapel and lets him know that they need to put his son in a medical coma. However, if they cannot solve the problem, he won't wake up. Chase suggests that he visit his boy before that happens. Rodney dons a bio suit and spends a few moments with Foreman before Cameron induces the coma. As she administers the IV, Cameron tells Foreman that she accepts his earlier apology.
Wilson implores House to perform the biopsy, dismissing House's claim that it is too dangerous. Wilson asserts that House doesn't spend time with patients because he'll get close to them. If it were anyone else, he would have drilled into their heads long ago. Cameron reports that the EEG shows that Foreman is still in pain. She demands they do the biopsy now. House still refuses. Cameron hands him the paper showing her legal proxy status.
Cuddy confirms that the proxy letter checks out. She instructs Cameron to proceed with the biopsy and ignore House's interference. Cameron remarks that Cuddy is no hero because they could have cut into a dead man's head long ago. Cameron then apologizes. House follows her out and begs for an hour. He wants to go back to Joe's apartment and to see if another animal died. The place was such a dump, there must be more vermin there. If House finds something, he can cut its head open instead of Foreman's. Cameron tells House that when Foreman's O2 stats hit 90, she must proceed.
House, not wearing a biosuit, again inspects the apartment. He notices a pigeon hit the window and the rooftop shed. The bird is blind. House stalks the bird, but it flies off.
Cameron readies the neurosurgery tools. Cameron calls House to announce that she is about to proceed, but House tells her that the water Joe uses for his marijuana might be the answer. Cameron already tested that water and it is clean. House is stumped. Foreman's O2 stats drop to 89, so Cameron starts the biopsy.
House follows the piping to a water tank. He quickly calls Cameron to say that they tested the wrong water. The tank he found is riddled with Naegleria. She already knows this because her biopsy showed the same results. House is dismayed.
Cameron finds Rodney Foreman to let him know that his son has primary amoebic meningoencephalitis, which is a parasite that goes through the nose and migrates into the brain. There it feeds on brain cells. It is treatable and will cause no lasting damage. However, they don't yet know if the surgery or coma produced any side effects.
Foreman gets transferred from isolation to the ICU. He comes out of the coma and doesn't feel any pain. House tests his vision and Foreman successfully follows his finger. House then asks Foreman to identify the people in the room. Foreman realizes that they performed the biopsy. He successfully names Cameron, his father and House. House then asks Foreman to wiggle his left toes. Although Foreman says he moved them, his toes remain still. House becomes concerned, and has Foreman raise his right arm. Foreman raises his left.