Rachel was a student at Arcadia Bay, Blackwell Academy staying in room 224 of the Prescott Dormitory. She went missing on April 22, 2013, while Mr Jefferson was still teaching at the academy. Given the nature of certain graffiti on and off campus, it is easy to get the impression that Rachel was quite promiscuous.
Rumors have been going around on campus that Rachel and Mr. Jefferson had a sexual affair. This information came to Stella Hill from a "good source," although this source remains unknown.
In Episode 5: Polarized (when you are in the Dark Room), Mr. Jefferson explains to Max that Nathan Prescott had accidentally overdosed her with a drug. In Episode 4: Dark Room, you can find Rachel Amber's body after you find the Dark Room at the Farmhouse, which then you go to Chloe and Rachel's (used to be with Rachel) Junkyard to see where Mr. Jefferson has put her body (which is buried on the ground).