It's a virus caused by the elements of harmony

Rarity was wearing her element constantly because of its beauty... well.. uhm It contaminated her body's natural harmony causing her to become hostile and to start decomposing slowly. the sickness is now known to spread through bites Stage 1: headaches, burning itching skin around affected areas Stage 2: loss of memory, hostile behavior, hair loss, infection spreading, bloodshot eyes Stage 3: body decaying, especially mouth and bitten area, extreme loss of weight, blindness, increase of hearing, cutie mark begins to blur, limbs begin to grow out Final Stage: organs begin to fall out, more mouth decaying, constant hunger, sight back and better than before, loss of color in coat and mane, loss of cutie mark and no longer recognizable also, Rarity's element is officially no longer a necklace and the small bit around the gem and the gem are now attached to her body and Rarity has been locked up in her boutique to prevent the spread