EDIT: It's been found. Thank you PMer who messaged me, found my search and wishes to be anonymous.
The story is Dirty Little Secret by PatchesOfInk http://www.fanfiction.net/s/6017682/1/Dirty-Little-Secret
I am looking for a multi-chapter FaBerry story. Quinn and Mercedes has seen a difference in Rachel and Quinn thinks she knows what it is.
They go to Rachel's house and confronts her and they discover she was raped and she has been trying to deal with it on her own.
When they go back to school Mercedes and Quinn has her back when David K. walks up to her and makes some rude comments Quinn and Mercedes see's Rachel scared and they put two and two together. Mercedes tackles David to the ground and starts hitting him.
Rachel is taken to the choir room. Quinn is trying to calm her down when she talks about her assault unknown to her that everyone and her parents is in the room.
In part of the story Santana goes to beat up David with Puck.
That's all I can remember I hope someone can help me thanks.