Eventually, Murphy can't take the nudging.
The fall finale ends with his punching the big cheese, fleeing the hospital, and then his apartment. The pressure to conform had been too much.
Either the world will have to accept him as different or he won't continue to be part of that world.
We won't know until January, when the series picks up again, where Murphy went, what he might have learned, what others might have learned, and if he will resume his surgical residency.
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