In universe, she was offered a position at Starfleet Medical. She worked with Calvin Hutchinson (the Commander that Data learned small talk in order to interact with in "Starship Mine"), but her actual role there was never explained. [According to Memory-Beta](http://memory-beta.wikia.com/wiki/Beverly_Crusher#Aboard_the_Enterprise-D), the (quasi-canonical) novels indicate she was actually the *head* of Starfleet Medical. When she returned, not a lot was said, but in "Evolution" it seems like she told Picard that she may have returned so that she wasn't separated from Wesley:

> PICARD: If you're concerned about Wesley, I see no evidence that there's a problem.

> BEVERLY: I know. In a funny kind of way... that's exactly my point. We talk. We smile. It's almost too polite.

> PICARD: Beverly, this is simply a matter of time. I know how difficult it was to be away.

> BEVERLY (vulnerable): Tell me about him.

Out-of-universe, according to some recent reports, there was some sort of problem between Gates McFadden and producer/writer [Maurice Hurley](http://en.memory-alpha.org/wiki/Maurice_Hurley). I've heard this characterized in some places as sexual harassment, but I'm not sure that's based on any actual allegations. Rick Berman did say he was at the center of it, though:

> Gates McFadden fired at end of first season because head writer Maurice Hurley "he had a real bone to pick" with Gates and din’t like her acting, Berman brought Gates back for 3rd season after Hurley left

(That quote is from the summary [here](http://trekmovie.com/2009/08/26/rick-berman-talks-18-years-of-trek-in-extensive-oral-history/).)

[This comment](http://www.trekbbs.com/showpost.php?s=c5ff170b5f349ad5b20ae933ff365c46&p=4787030&postcount=19) also cites her hair (of all things) as costing lots of time and money to keep styled right to avoid continuity problems. Not sure I buy it, but there it is.