"McFadden left the series during the second season, replaced by Diana Muldaur as Doctor Katherine Pulaski. Officially, the producers felt that the character of Crusher had not developed as well as they had hoped. Unofficially, there were some disagreements between the show's producers and McFadden as to how the character should develop, which may have led to some bad blood between her and several executive producers, resulting in McFadden's being released from her contract before the second season." - excerpt from Memory Alpha: Gates McFadden.
Off the official record, I heard that she alleged sexual harassment against someone on the staff and left when nothing was done, but he was gone by season 3 so when Muldaur wanted off they brought her back. "Bad blood" may be an attempt to say that inderectly.
The correct answer is: Because she was pregnant.
The late Herbert J. Wright cited Hurley as one of the reasons he left TNG. He described Hurley as "basically playing drinking buddies with Gene." (Captains' Logs: The Unauthorized Complete Trek Voyages, p. 224) Tracy Tormé also named Hurley as one of the causes of his departure, after numerous disagreements over Tormé's scripts. (Captains' Logs: The Unauthorized Complete Trek Voyages, pp. 170, 177-178, 181-182)
According to Rick Berman, Hurley was the reason behind Gates McFadden's departure from The Next Generation in its second season, as he disliked her acting and "had a bone to pick with her." After he left the show in the third season, McFadden was invited back by Berman. 
I remember her being on the show while she was pregnant. They just covered it up with her smock ProfessorTrek 16:47, August 23, 2011 (UTC)
She was pregnant during the show's fourth season, so that had no bearing on her absence during the second season. Quornhog 12:20, October 13, 2011 (UTC)
Yes, Her son was born in 1991.
My mom told me about that. Apparently she was in "The Hunt for Red October" for about 5 seconds and that's why we got Pulaski.
Actually the real reason is that she had uncontrollable bouts of irritable bowel syndrome during the early seasons of TNG which made her emotional and also frequently interrupted shoots. I understand she took some time off to deal with it. My friend was on the production crew.
- Funny how your "friend" seems to be the only one aware of this information, which is not mentioned anywhere else and without something to back it up is just unsubstantiated innuendo and rumor. 31dot 01:55, May 14, 2012 (UTC)
== This question pops up at least twice a month here, I suggest that you check her page at Memory Alpha for clarification. Basically she was not satisfied with the way here character was being developed during the first season and there was some bad blood between her and the producers. She wasn't the only cast member to complain about this; Denise Crosby, Marina Sirtis, Micheal Dorn, and LeVar Burton had apparently made similar complaints, Denise Crosby of course left before the first season even ended.-Cpthunt (talk) 07:51, August 14, 2012 (UTC)
== Gates McFadden left Star Trek because she was dealing with personal issues such as diverticulitis and spastic colon, as indicated in the Popular Pages section here. 22.214.171.124 00:42, April 4, 2013 (UTC)
Based upon sources the leading reason for the departure for one season was to deal with the colon problems Gates was suffering from causing explosive diarrhea which left many feeling uncomfortable.