Located in the rebel aqueducts (also findable with CTRL+F). To get to the aqueducts, you can jump down the well in the very far northeastern part of the zone or use the portal in the far north-central wall of the zone, or the portal just northeast of the arena. (For mapped locations to the aqueducts, see this image.)
For all things Rain of Fear, check out this overview of the expansion.
Kilithyr also appears in both Chelsith group missions, as well as the raid: