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Stacy Warner returns to PPTH, having been officially hired as the hospital's General Counsel. House eventually realizes that he still has feelings for her. In an attempt to prove that she feels the same way about him, he breaks into her therapist's office and reads her file. House learns that she is not sleeping with her husband Mark Warner. He tries to get back with her by killing a rat that has invaded her home, but soon changes his mind after learning that the rat has an illness that brings out the diagnostician in him.
As House and his team diagnose Vince, a man with a giant, swollen tongue, a disgruntled former patient Jack Moriarty walks into House's office and shoots him. House continues treating his patient from his ICU hospital bed with Jack, who hospital security shot and hand-cuffed to his bed, as his roommate. When the after-effects of the shooting begin to impact House, he starts to question his ability to diagnose correctly. As his patient's body deteriorates, House struggles through his self-doubt and must trust his team to find a way to solve the case.
A 16-year-old Hurricane Katrina victim suffering from hallucinations due to the tragedy is brought to House by his former bandmate, Crandall, who recently found out the girl is his daughter. Although House fears his friend is being scammed, he takes the case. As he works his way through the girl's lies so he can diagnose and treat her, he's forced to tell a few lies of his own. Also, Cuddy looks for a sperm donor.
When young mother, Kara, has a seizure while bathing her child, it causes the near drowning of her newborn son. Unable to determine the cause of Kara's seizures, House and the team race to find what's wrong with her while simultaneously trying to bring her infant back to life.
Foreman continues to experience the same dire progression of symptoms as the dead police officer: blindness, muscle contractions, and excruciating pain. When he realizes he may be facing imminent death, he calls his father and tries to make amends; his father comes to his son's side. As it comes down to a race against time, House believes the solution to the illness is in the police officer's apartment. House tries radical procedures to save Foreman's life.
When a police officer with a gunshot wound to the head and uncontrollable laughter is admitted, House and the team are baffled. When Foreman begins showing the same bizarre symptoms, they race to determine the cause of the illness before Foreman's condition takes the same path.
When 15-year-old faith healer, Boyd, is admitted and claims he can talk to God, House takes the case. House thinks the kid is a clever con until the boy touches one of Wilson's cancer patients and causes her cancer to go into remission.
A young woman, Hannah, hasn't been able to sleep for 10 days. She's brought in after she downed an entire bottle of sleeping pills and still didn't fall asleep. Meanwhile, Cameron accuses Foreman of stealing a medical journal article she wrote, which Foreman denies.
It's poker night at Princeton Plainsboro when the hospital hosts an oncology benefit. A 6-year-old boy is brought in exhibiting symptoms that aren't too unusual; however, when House learns of additional specifics, he jumps on the case right away.
6 months after a teenage girl crushes her chest in a car accident and receives a heart transplant she goes into anaphylactic shock in her clean room bedroom after her boyfriend visits.
House and his team take on a new patient, Bob, who comes to Princeton Plainsboro Teaching Hospital after suffering from a breathing attack while role-playing in the bedroom with his wife. The symptoms point to heavy metal poisoning, but the tests do not. House believes a woman is trying to kill her husband and tries to find the proof to confirm his suspicions. When Wilson moves in with House after separating from his wife, he learns Wilson is a great cook.
When Henry experiences a seizure but is not aware of it while it's happening, House takes on the case. The team's differential diagnosis points to a bacterial infection, but Henry suffers a heart attack before the treatment for his infection can work, prompting the need for a heart transplant. Then, the team races to diagnose a dead woman's illness so they can harvest her heart to save their living patient.
House and his team work to treat a teenage supermodel for heroin addiction and, in the process, uncovers a startling secret about the girl.
House and his team have a difficult challenge when a teenage boy enters the hospital severely burned with unusual blood-test results. How can you diagnose a burn victim when you cannot use standard testing methods? House makes himself the guinea pig in his own unofficial tests of a new drug designed to treat migraines to prove a former medical school colleague is wrong about the drug.
Margo, a young housewife on fertility medication, is brought to Princeton Plainsboro Hospital when her inexplicable muscle flailing causes her to crash her car. House and Stacy try to resolve their relationship issues once and for all. Cameron refuses to take her HIV test, wary of the results.
Journalist Fletcher Stone collapses at his editor's retirement party and hits his head on a desk. His sentences are garbled and incoherent when he regains consciousness, so he is rushed to Princeton Plainsboro Teaching Hospital. House and Stacy are out of town defending House's Medicaid billings and later stranded at an airport due to bad weather. So, the team struggles to solve the case on its own.
Off-track betting gambler Anica collapses in front of House while both follow horse races at the site. Confused by her symptoms and what he witnessed after she collapsed, he instructs medics to take her to Princeton Plainsboro and takes her case. With Foreman temporarily House's supervisor, the team must figure out if Anica, who cried wolf many times, is really ill.
Kayla, the mother of two young girls, doubles over with stomach pain during her children's talent show and is rushed to Princeton-Plainsboro Teaching Hospital. Six months later, Stacy counsels Dr. Chase and Dr. House in preparation for a disciplinary hearing to determine if either Chase or House made a mistake that ultimately led to Kayla's death and her family's subsequent lawsuit. She soon realizes Chase is holding something back.
Kalvin, a gay man with full-blown AIDS, confronts House in front of his home, demands that House figure out what's causing his illness - besides HIV or AIDS - and collapses at his feet, going into shock. When House discovers the man's father is suffering from symptoms of his own, he must determine any connection to save both their lives. Meanwhile, Cameron faces a potentially life-threatening disease of her own.
When a famous professional cyclist is brought in after collapsing during a race, House doesn't want to treat him because he thinks he's lying about doing drugs. But when the patient is forthcoming about taking all sorts of performance enhancers and blood-doping drugs, House is definitely intrigued.
A graduating Princeton student suffers a seizure from internal shocks while partying at a frat house and is rushed to Princeton Plainsboro Hospital. With his father Ken at his bedside, it becomes apparent the two haven't been truthful about their lives with each other. Their trust issues prevent the medical team from getting the necessary information to diagnose and treat Carnell's illness. Also, House's parents drop by to see their son.
When Dr. Sebastian Charles, renowned physician and head of an international organization to fight the spread of tuberculosis among the poor in Africa, is rushed to Princeton Plainsboro Teaching Hospital after collapsing, he immediately determines all the symptoms are from TB. Dr. House has a different opinion and requests additional tests to help determine the cause of his illness.
When Cuddy's handyman Alfredo, a young Latino and the sole provider for his family, falls from her roof and develops strange darkened pinkies, Cuddy joins the team in trying to figure out what's wrong with him.
A 9-year-old terminal cancer patient, Andie, suffered from a hallucinogenic episode and was admitted to the hospital. Wilson convinces House to take the case, but he and his team struggle to diagnose what caused the hallucination. The young girl handles her illness so well that House wonders whether she is really that brave or if it is a medical symptom.
When Death Row inmate Clarence mysteriously and suddenly collapses after hallucinating, House jumps at the chance to take the case for its difficulty and because it's "cool" over Cuddy and Foreman's objections. Dr. Cameron refuses to treat the patient in protest and feels they should treat a cancer patient because she's more deserving, raising the question: is one life more important than another? Also, House must now work closely with Stacy.
House starts the year in prison, serving out a long term for his various misdeeds in Moving On. However, it turns out that he didn't even try to get a lesser sentence and took a one-year term without complaint. He blows a chance for early parole in order to prove a fellow patient's diagnosis. Although he plans to withdraw from the practice of medicine, it appears the real co-dependent relationship is between House and the hospital. With House looking at serving at least another six months, the new Dean of Medicine, Eric Foreman approaches House with an offer to return to work.
House and Cuddy make their relationship public, but despite the fact that they are both happier than they have been for years, they both see problems. House is sure that Cuddy is merely hopped up on the sex and good feelings that are typical early in the relationship and that she will dump him once she realizes what she's gotten herself into. Cuddy is sure that her supervisory role over House is either going to poison their relationship or ruin House's medical skills, and she's uncomfortable with many aspects of House's past, such as the prostitute he's still seeing for non-sexual purposes. House is also not certain he wants to have a role in Rachel Cuddy's life and starts to balk at the responsibility, although towards the end of the season, House and Rachel seem to share a strange bond over a cartoon about pirates.
After finally realizing that his Vicodin habit is distorting his view of reality, House voluntarily enters Mayfield Psychiatric Hospital to detox. However, detoxing turns out to be the easy part - House can't get his medical license back until he's willing to admit his problems run deeper. Although he resists at first, he finally gives in. At the same time, he falls in love, but then finds his paramour has no further interest in him. When he turns to his doctor instead of Vicodin for help, Dr. Nolan realizes he's ready to return to the practice of medicine.
Wilson slowly starts to recover from Amber's untimely death, but begins to reevaluate his life and to contemplate resigning from his post at the hospital. House's original regret over his role in Amber's death seems to have worn off as instead of being supportive, he merely tries to convince Wilson that he is overreacting to the situation. However, Wilson winds up leaving his post.
After losing his original diagnostic team, House decides that he doesn't need fellows as he feels that he can handle a case all on his own but after taking a long time to solve a case, Cuddy insists that he start looking for possible doctors to join his new team. House grudgingly accepts and gets forty applicants together and has a reality show style contest to see which lucky three applicants will stay on to get the vacant fellowship openings. Meanwhile, Cameron and Chase come back to work at the hospital, while Foreman starts work in a job similar to House's at another hospital. However, Foreman is soon fired for doing exactly what House would do and winds up back at Princeton-Plainsboro. House wants nothing to do with him, but Cuddy insists he can only hire two new fellows and must have Foreman on his team to keep an eye on him.
House recovers from his gunshot wounds, but despite his pain temporarily disappearing and the fact that his leg is working again, he is soon back on Vicodin. He runs into a particularly difficult patient at the clinic, who turns out to be a police officer, who then makes it his business to get House sent to jail for possessing Vicodin illegally. Unfortunately, House has used Wilson's prescription pad to forge his own prescriptions, even though Wilson has been supplying him with Vicodin freely. House nearly goes to jail, but Cuddy then perjures herself in court to have the charges dismissed.
Stacy Warner returns to PPTH, having been officially hired as the hospital's General Counsel. House eventually realizes that he still has feelings for her. In an attempt to prove that she feels the same way about him, he breaks into her therapist's office and reads her file. House learns that she is not sleeping with her husband Mark Warner. He tries to get back with her by killing a rat that has invaded her home, but soon changes his mind after learning that the rat has an illness that brings out the diagnostician in him.
We are introduced to the brilliant, famous but extremely exasperating Gregory House. We learn that despite his considerable intellect and talents as a physician, he does next to no work at the hospital, merely coming in from 9 to 5 to oversee his three teaching fellows. This infuriates his boss, Dean of Medicine Lisa Cuddy. However she keeps him on because when the rest of the doctors are stumped, House swings into action.