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A church was a building used for worship and other religious activities. By extension, the word also was used to refer to a specific sect or religion.
In the 1970s, the Dæmon Azal located himself within a church in Devil's End following a confrontation between the Third Doctor and the Master. His ultimate defeat by Jo Grant led to the church's destruction. (TV: The Dæmons) The Master had hidden his TARDIS — disguised as the Stone of Sacrifice — in the remains of the church and went to retrieve it after his escape by hovercraft. (PROSE: The Eight Doctors)
A sentience inhabited a church in the town of Cheldon Bonniface. Known as Saul, he inhabited the church and was able to exert an amount of influence on the church's congregation. (PROSE: Timewyrm: Revelation)
Several churches were places of significance on Earth, not just as meaningful locations of worship, but in other guises. St Mary's Church in Cardiff was used as a location to hide a resurrection gauntlet. (TV: Dead Man Walking)
After the Reapers attacked, the Ninth Doctor shepherded attendees to the wedding of Stuart Hoskins and Sarah Clark inside a church. The age of the walls meant the assailants couldn't gain immediate access. (TV: Father's Day)
Receiving a phone call from her mother in 2009, Donna claimed to be in church praying. In reality, she was sat on a toilet within a cubicle while investigating Adipose Industries. (TV: Partners in Crime)
Wilfred Mott visited a church and was spoken to by a woman. The woman told him that the church had been a convent which a man in a blue box had saved from a demon which had fallen from the sky. The man was called "the sainted physician" and the blue box was pictured on a stained glass window in the church. (TV: The End of Time)
When Cardiff went blind, Colin Colchester-Price gathered as many people as he could at St Martin's at the top of Avery Road. When Jack Harkness arrived, the people attempted to steal Jack's gun and night-vision goggles, prompting Jack and Colin to leave. (AUDIO: See No Evil)
Religions that were referred to as churches
The Church of the Outsiders was a cult founded by Steve Ross and, after his death, led by Val Ross. It originated in the United States of America and was not recognised as a religion by UK law. Its core belief was that humans had to breed with aliens in order to evolve. (AUDIO: Believe)
The Church of the Grey was founded in the early 21st century. This church went through several reformations during the religious upheavals on the planet Dellah in the 26th century. (PROSE: Where Angels Fear)
The Church of Maa'lon also existed around the 26th century and underwent a significant increase in followers on the planet Dellah. Several of its members met a being claiming to be Maa'lon. (PROSE: Where Angels Fear)