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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 remains inhibited by injuries sustained from a bus accident that has also left a victim rapidly deteriorating from a mysterious condition. Clues inside House's head hold the key to a patient's condition, and House's friendship with Wilson is tested beyond limits as murky memories from the bus accident the night before threaten to change their lives forever.
House finds himself dazed, confused and covered in blood after surviving a bus accident that left dozens seriously injured. Unable to clearly recall the events leading up to the crash due to his head injuries, House becomes convinced through his flashbacks that a fellow bus passenger was exhibiting signs of a deadly illness prior to the crash.
House is convinced one of the actors on his favorite soap opera "Prescription Passion" has a serious medical condition after observing his symptoms on television. House decides to intervene and take matters into his own hands.
House suspects an emergency room patient has a bigger problem then the ER initially diagnosed based on the fact that the patient is too nice. A skeptical House questions the patient's sunny disposition as the team tries to get to the bottom of his illness. Meanwhile, House and Amber are at odds about how much time they each get to spend with Wilson, and Cuddy demands House give his team performance reviews.
House and the team encounter a woman admitted to Princeton-Plainsboro after she collapsed at her wedding. Her test results come up negative for a variety of common diseases, which leads the team to suspect foul play. Meanwhile, House is preoccupied by Wilson's newly-outed relationship with a woman whose personality is remarkably similar to House's.
When Dr. Cate Milton, a psychiatrist trapped at the South Pole and the research station's only doctor, becomes ill in the middle of her assignment, she and Dr. House are thrust into a long-distance relationship of sorts. Unable to get Cate out or any additional medical supplies to the South Pole station, House and his team must resort to treating her via webcam.
House and the team treat a woman who suffers from a sudden paralysis of the hands that causes an injury to her daughter while she's spotting her at an indoor rock-climbing wall. As House probes the woman and her injured daughter for any leads as to what might be causing her condition, House is convinced that the woman is withholding information.
When Cuddy puts the pressure on House to choose the final members of his team, House deliberately assigns the candidates to a particularly challenging case - an uncooperative, over-the-hill former punk rock star with a history of drug abuse and civil disobedience.
House encounters a magician whose heart failed while performing an underwater escape act, nearly drowning. While the remaining fellowship candidates work to diagnose the illusionist, House is determined to prove that he's a scam artist faking his ailments to cover up his own incompetence. Meanwhile, House pits the fellows against each other in his version of an immunity challenge.
A documentary film crew chronicles a teenager with a major facial deformity who opts to undergo a dramatic reconstructive procedure. When the patient suffers a heart attack just before the surgery, House and the fellowship candidates must determine the cause since the surgery cannot proceed until the patient's cardiac condition is diagnosed. The film crew and the candidates, following around House, distract him.
House is recruited by the CIA to help diagnose a deathly ill agent with an unknown illness. Meanwhile, Foreman faces resistance from the remaining six fellowship candidates when they question his judgment and argue over the diagnosis of a female drag car racer who passed out after a race.
The team takes on the case of a man who collapsed while being mugged. When the man complains of new symptoms that do not fit his initial admission profile, the team suspects he is a hypochondriac. As Mr. X continues to fall ill with symptoms unrelated to his neurological disorder, Foreman and the remaining six fellows are assigned to keep watch, and are bemused as they see their own behavioral idiosyncrasies reflected through him.
When a 20-year-old funeral home cosmetician, Irene, has a massive seizure, she hallucinates the cadavers in the funeral home have come to life, House and the remaining seven fellowship candidates must figure out why.
The final 10 fellowship candidates compete ferociously when House splits them into two teams by gender. They are assigned to diagnose and treat a wheelchair-bound man with muscular atrophy who is slowly suffocating.
House has relented to interviewing potential team members, but he's doing it his way. He called in all 40 applicants for the open three positions on his team and puts them to the test in a Darwinian trial period. As he drills the fellows and arbitrarily fires some along the way, an Air Force fighter pilot named Greta asks him to secretly treat her. She is a candidate for NASA's astronaut training program. House sets the applicants against one another to help treat the pilot with an unusual neurological disorder.
With his diagnostic team gone, House tries to diagnose Megan, a young woman who survived an office building collapse. Due to her injuries, Megan's only form of communication is blinking. With her condition worsening, Cuddy puts pressure on House to hire a new team, but instead, he attempts a differential diagnosis with help from the janitor. Wilson resorts to desperate measures by kidnapping House's guitar.
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.