A young boy named Clancy refuses to go to sleep and thinks "they" are out to get him. He turns on his TV. Suddenly, the channels begin changing and the room begins to rattle. A blindingly white light comes into the room. In the morning, Clancy's father Todd finds his son on the front lawn, face down. A large blood spot is on his behind.
House laces up for another jog. After leaving the house, he immediately comes back inside, grabbing his leg. He limps into the hospital. Cuddy and Wilson notice this, but House ignores them and takes the elevator instead of the stairs. Cuddy worries that House is depressed about his last case, causing him to slack on rehab. Wilson emphasizes that House only made a lucky guess. He still doesn't think they should tell him that the cortisol worked.
The team introduces House to Clancy's case. Cameron theorizes that rectal bleeding and alien abduction sightings are most likely sexual abuse, because trauma can cause the fantasy. Foreman deftly points out that the ER found no evidence of rectal tearing, semen or pubic hairs. House, rejecting hallucinations as a possibility, asks for a full set of coagulants and endoscopies from both ends.
Chase nicks Clancy's arm to time how long it takes him to stop bleeding. He clots with no problems. Clancy asks if the windows are locked because "they" know he's in the hospital. "They" put a chip in his neck to keep track of him that Clancy can feel. Chase pinches Clancy's neck with forceps, pretending to remove the chip. Clancy doesn't buy it.
Foreman and Chase report that both endoscopies were clean and the bleeding test was fine. House wonders if Chase screwed up the test. Later that night, Foreman tells House that he performed another bleed test on his own and it took twenty-five minutes to stop the bleeding. Cameron sensibly suggests running labs to check Clancy's clotting factors. Chase heads to Clancy's room for the new test. The boy is missing.
Chase finds Clancy in the men's room. He claims that he needed a windowless room so he could remove the chip. Chase cleans up the massive amount of blood from Clancy's neck and realizes there is something metal in the gash.
The metal is titanium from a surgical pin inserted into Clancy's broken arm from four years ago. House thinks that a small piece broke off and migrated. Chase finds it hard to believe that titanium could break. Even if it did migrate, how would it end up in the neck? House is more interested in the fact that Clancy cut open the back of his neck and clotted without bleeding to death. The case has changed from no bleeding disorder to a bleeding disorder and then back to being fine.
The team performs yet another blood test on Clancy. His mother, Stephanie, wonders if this was all in his mind because he had been looking for an alien tracking device.
Cameron receives a file on a returning patient and is stunned to find out that it's Richard McNeil, the paralyzed patient that House supposedly could not fix. McNeil is walking with assistance. He was afflicted with Addison's disease, and the cortisol shot turned his brain on like a switch. Cuddy comes in, dismayed to see that the patient she's been trying to hide from House is now out in the open.
Clancy suffers a pulmonary edema when blood is being drawn. Doctors rush in and frantically work to bring him back to life. Clancy holds steady but has a high blood pressure. Foreman discovers that Clancy does have a blood disorder, but it is von Willebrand disease. The doctors are baffled by the inconsistent test results. Cameron, referencing the high blood pressure, wonders if it is connected. Hypertensive crises can activate clotting factors.
They perform a transesophegeal echo to identify the problems in Clancy's heart, but the echo reveals nothing. House, determined to find something, insists that a small part of the heart isn't beating along with the rest. His team is unimpressed by a basic arrthymia. House instructs them to bring him a sample of the non-beating myocytes.
Cuddy tells House that she wants to do a PET scan on him to determine if his increasing leg pain is a positive or negative sign. House assures her that if he thought his leg was deteriorating, he would've been taking preventative measures by now.
Chase compares Clancy's DNA against the DNA taken from the heart. They don't match. House is at a loss for words. The team sequesters in the office for a differential. Wondering if the alien DNA is confined only to the heart, Cameron suggests introducing an antibody that recognizes only the protein from the other DNA and flush it through the body. If it shows up anywhere else, they will be able to find the DNA in other parts of the body.
They administer a PET scan on Clancy and spot a clump of affected cells in the bone marrow of the boy's femur. They also spot more cells in his heart and left eye. However, there is nothing in his brain, meaning Clancy's problem is not neurological. Surgery begins to remove the abnormal cells from each area. The normal tissue will begin to replace the removed areas and Clancy should be fine in time.
Wilson finds House in his office and tosses him a bottle of Vicodin. If he's so sure his leg is fine, why not take the pills so he can get through rehab? Wilson remarks that, lately, House hasn't always been right. Later, House hits the treadmill but runs with a noticeable limp. He gives into the pain and pops a couple of Vicodin. This allows him to keep jogging.
Clancy is asleep when the hospital room begins to rattle and the white light reappears in the window. Clancy floats above the bed. In reality, he is having a seizure. Chase rushes into the room as Clancy flails wildly.
The next morning, Foreman reports that the hallucinations and seizures indicate problems in the temporal lobe. Figuring that their antibody tag didn't penetrate the blood brain barrier, House asks them to go straight into the brain. Yet another PET scan of the brain is totally clean. House wonders if it's possible that something is there, but the antibody isn't affecting the brain proteins, which have a different cell structure. House retreats to his office to think in private.
After some deliberations, House instructs the team to send Clancy home. If they removed the affected cells and the brain was clean, there's nothing more they can do. Cuddy rushes to catch up with House in the parking garage, demanding to know why he's giving up on Clancy. House, knowing that Cuddy is displaying an unusual level of interest in his patients lately, asks what she's hiding. Cuddy admits that House was right about McNeil's case. A single shot of cortisol cured him. House thinks about what this means, mocks Cuddy for needing in vitro fertilization, and then is hit with a revelation.
Barging into the office, House asks his team how a person could end up with two strands of DNA. Referencing Stephanie's in vitro treatments, House asks if Clancy could be a twin. Two embryos in the IVF treatment bonded and Clancy is two people in one, a condition called chimerism. Now they have to cut out the second strain of DNA, some of which is in the brain.
Believing that the alien DNA was causing the visions, House plan to stimulate a hallucination during brain surgery. This will cause the secondary cells to light up so they can be removed. Both the plan and the surgery work perfectly.
House tracks down Wilson in order to gloat. He makes it clear that he beat their little scheme. Yet when he returns home alone, House pulls out one of his canes and starts using it.