Sci-Fag relates to all members of Scientology being disliked. The original root word "Fag" comes from the word faggot, which means bundle of sticks. The bundle of sticks is refering to the sticks that people would collect before they were burnt at the stick, so the word fag or faggot is a violent and obscene way of saying I want you to be burned at the stick.
"So i heard you like mudkips?" - He didnt say anything he must be a scifag.
"Zomg look at that scifag trying to take photos of us"