Bosses
Some you find, some you build. A chamber's boss comes with the room you placed, and six of the minibosses are summoned by your own rooms reaching tier 3.
The temple's end
Atziri Behind the Royal Access Chamber — a Restricted Room, so the Architect has to fall first. IAtziri, the Red QueenIIAtziri, the Fell Serpent
Xipocado, Royal Architect Defeating him opens Xipocado's Console, which places Restricted Rooms — and destabilises more of the temple on the way out.
Summoned by your rooms
A room reaching tier 3 adds these to the temple itself.
Room bosses
One per chamber. Flesh Surgeon and Commander have two each.