Basically, he had a heart attack, but in his leg. It took them three days to find the clot, and a lot of the muscle in his leg died. It's one of the most painful things to experience. Cuddy was his doctor, and his live-in girlfriend (Stacey) wanted him to amputate. He wanted to keep his leg. They removed the clot, but the pain didn't get any better. House asked to be put into a chemically-induced coma to sleep off the pain, and when he was under, Stacey was his medical proxy and chose to have the dead muscle removed. It was a middle ground - he kept the leg, but the dead cells were removed.
Watch the episode "Diagnose a Leg" (or whatever it's called) from Season two. It explains everything. Oh yea, did you see the episode where he got shot and Cuddy gave him Ketamine? That one showed how his pain was lessened for a while. Inbox me if you haven't seen it. I lovelovelove talking about this show. [ LM's advice column | Ask LM A Question ]
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