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The tribes that formed the Twelve Colonies had many temples on their worlds. A logical presumption is that the remnants of humanity that comprise the Fleet had opened temples aboard their ships for worship after their homeworld temples are destroyed by the Cylon attack. Clergy such as Brothers, Sisters, priests, and oracles are presumed to be the central celebrants during formal services and hold counseling there. Colonials can also visit temple on their own for private worship.
On New Caprica, temples are created within tents. With the Cylon occupation of the planet, the human resistance uses a temple to hide what weapons they can gather in boxes that form an altar of a temple, knowing that the Cylons have respected the Colonials' sacred places and have not searched for weapons in temples.
A temple's altar may be decorated with stones, candles, tiny idols representing a Lord of Kobol, an piece of animal fur, and a dish containing polished stones, perhaps offerings to the gods from the meager resources that New Caprica provides. Temples were likely decorated more elaborately on the Twelve Colonies.
The Thirteenth Tribe created an expansive temple on an unnamed habitable planet known in the Sacred Scrolls as The Temple of Five. It is discovered mysteriously by Galen Tyrol, the son of a priest and an oracle (TRS: "The Eye of Jupiter").
A temple is made on Galactica herself after the Fall of the Colonies. This temple is created by Brother John Cavil and is used as a meeting place for other Cylons in the Fleet, where many of the initial attempts at disrupting the Fleet are planned (TRS: "The Plan", "Litmus", "Six Degrees of Separation"). Despite the Cylon connection, this temple is later re-appropriated by Colonial citizens and is used for Callandra Henderson Tyrol's funeral service, as well as later desecrated by Gaius Baltar and his religious group's harem (TRS: "Escape Velocity").