Celestial Emissary is an optional, nearly end-game boss, and reaching him is a bit cryptic. You need to at least kill Rom to trigger the blood moon and return to Yahar'gul. Upon your re-vist, find the Upper Cathedral Key on the dead Choir member sealed in the cage (there is a cleft in the right wall immediately before the witches in front of the Amygdala that shoots lasers at you; go down that to drop into the cage). Once you have the key, warp to Cathedral Ward lamppost and go through the door on the right and take the lift up to Old Church Workshop (where you probably found the Radiant Sword Hunter Badge much earlier). From there, keep going up and unlock the door with the Upper Cathedral Key. After claiming the Orphanage Key from a Brainsucker there you can open the gate into the garden, where he will await you. He is also the 2nd boss in the Great Isz Chalice (obtained by killing Ebrietas, who you access by breaking the Cathedral window from the garden where you first fought the Emissary).