Fanfiction is decidedly outside canon. Somebody could write some fanfic in which Rose Tyler has a child by a dalek, but subsequent episodes of Dr. Who would not have to include that child. Somebody writing officially for Doctor wouldn't be allowed to do that unless it fitted in with the official story arc.
If it's too far off canon, it's called AU (alternative universe). Canon is the basic 'facts' of the characters and their circumstances. Fanfic, while taking the characters into new adventures, generally stays within canon - what happened in the show is part of the backstory and it's expected that you (the writer) will abide by canon. If you contradict it, you'll definitely get called on it (sometimes ferociously) unless it's stated at the outset that it is AU or that you are deliberately doing it for that particular story.
