In the season pilot, you may remember, House diagnoses a supposedly disassociated, wheel-chair bound man with Addison's Disease, but no one indulges him. The point of bringing this up is because Cuddy eventually gives the man the cure House suggested. It works, but Wilson tells Cuddy to lie to House about it so as not to feed his ego further.
Also, we observe at episode's end that House steals a prescription pad from Wilson's desk, indicating he is beginning to feel pain in his leg again.
The repercussions of House's believed failure cause him to lose confidence in his next case, but when he discovers the lie he suddenly has a revelation about his current case and solves it.
Confidence is restored, but he begins to use his cane again. It is in another episode this season where it is opined that House may have Asperger Syndrome, which would explain his lack of boundaries, off-the-cuff speech, and dislike of change.
One day in the clinic House sees a man named Michael Tritter who complains of a rash on his genitals, and wants House to take a swab and test it. House pops a Vicodin and tells him there's no need, since it was probably caused by dehydration from the nicotine gum he's chewing. As House tries to leave, Tritter kicks his cane out from under him, and berates him for being arrogant. So House takes the swab, then sticks a rectal thermometer in his butt, and instead of coming back he leaves for the day.
Later Cuddy calls House into her office, where Tritter smugly waits for an apology. He very plainly informs House that what he really wants is to humiliate him "so he'll think twice about his actions". House refuses and leaves.
At the end of the episode there is a brief scene of Cuddy looking at a negative pregnancy test as House is headed home on his motorcycle. House is pulled over by a police car, and out steps Detective Tritter. Frisking House roughly, he takes a handful of Vicodin out of his jacket pocket and arrests him. Payback's a bitch.
Wilson faithfully bails him out the next day. Later that day Tritter shows up at the clinic to give House another ration of shit, but as usual the good doctor is up to slinging it right back. That evening Tritter breaks into House's apartment with a search warrant, finds bags of Vicodin bottles, and sites the inclination of a DA to feel that House compiled that much so as to traffic it.
House refuses to plea bargain, so it looks like it's going to court. Later, Tritter meets with Wilson, showing him dozens of possibly forged prescriptions from the pad House stole in the first episode, all with Wilson's signature. Wilson is caught off guard and is a terrible liar, but he refuses to say it isn't his signature, even though they aren't good forgeries.
Tritter begins to question House's team, and they all decide not to cooperate. Meanwhile, Tritter has Wilson's accounts frozen as part of the investigation. Then he has Wilson's license to prescribe medicine taken away, all in an obvious attempt to put the squeeze on Wilson.
Tritter also freezes the team's accounts and tries to play them off on each other to get them to rat House out.
Cuddy has been rationing Vicodin to House, and this is causing him to be distracted. A nearly disasterous diagnosis, a punch to Chase's jaw, and cruelly telling Cuddy what a terrible mother she would make are the results in quick succession. After that, Wilson goes reluctantly to Tritter.
House refuses the deal Wilson sets up with Tritter (two months in rehab on low strength pain killers). Cuddy then removes him from his current case and cuts him off of Vicodin.
House picks up a prescription of Oxycodone meant for one of Wilson's deceased cancer patients, so when Cuddy comes to him with Vicodin and a plea to return to the case she pulled him off of, he cheerfully refuses the Vicodin but gets right back into the case.
It's Christmas Eve. House is alone in his apartment and he calls his mom, leaving a message on her machine. He is mixing the Oxy with alcohol, in a possibly suicidal move. Later, Wilson comes to check on him, and finds him semi-conscious after throwing up the pills. Wilson leaves in disgust.
Later House comes to Tritter (alone in his office on Christmas Eve -- hmmm) and tries to take the deal, but Tritter coldly tells him that the deal is off, because he now has proof that House stole the Oxy.
House later tries to give Tritter the apology he wanted in the first place, but Tritter now claims that all he cares about are House's actions. So House checks himself into rehab, and apologizes to Wilson for what he put him through. When Tritter comes to see for himself, he still refuses to drop the charges, saying that even House's actions lie.
During the court proceedings, House takes a call from his team on the current case that causes him to leave court under threat of contempt by the judge. In House's absence Cuddy takes the stand and lies, saying she had knowingly replaced the Oxycodone with a placebo. The case is dismissed, Tritter is told to leave House alone, and House is ordered to a night in jail for contempt.
Cuddy is furious about having to commit perjury, and Wilson discovers that the supposed low grade pain pills House was getting in rehab were in fact Vicodin (which he had bribed his supervisor to slip him.) Nothing has really changed, except that the apology to Wilson appears to be genuine.
While treating a rape victim, House reveals that his father abused him as a child (physically and psychologically, not sexually.)
Cuddy worries that she may be falling for House, and Chase and Cameron start having non-committal sex. Also shown in a couple of episodes is House covertly looking for some alternative to living with pain and taking pain pills.
Foreman, concerned that because of the way he has been treating patients he is becoming too much like House, says he is resigning. Wilson sneaks anti-depressants into House's coffee, which make him happy but unable to effectively diagnose his patient's problem. So, anti-depressants are not the answer.
During Foreman's "two week notice" period, House secretly sabotages at least one interview. Wilson accuses House of doing so because he can't handle change. So when House starts agreeing with whatever Foreman diagnoses for their current case, Chase confronts him about it being a sloppy ploy to get Foreman to stay. So House fires Chase.
House clumsily tries to talk Foreman into staying, but Eric's mind is made up. After Foreman leaves, Cameron comes to House and tenders her resignation. House is sans team. And thus ends Season 3. =)