The opera will be performed by more than 65 musicians from the BBC concert orchestra and is the result of a creative relationship with The Royal Opera House.
Text messages on the day of each event will summon selected members of the public to a secret railway location to form the flashmob and join in.
Stuart Murphy, the controller of BBC Three, said: "Flashmob – The Opera is a real first, which means it is a real risk -- just what we love doing on BBC Three."
Other highlights of the autumn schedule include a new series of hit comedy series 'Little Britain', starring Matt Lucas and David Walliams.
Comedy drama 'A New Life in Film' stars Kris Marshall from 'My Family' and 'Love Actually' as an enthusiastic film-maker with an overactive imagination.
BBC Three will also run a season of thought-provoking documentaries on living with cancer.
'You, Me and Cancer' is designed to raising awareness and understanding of the disease.
'Breast Cancer: The Operation' will show a live mastectomy for the first time on TV. The program follows a patient from when she first discovers she has the disease through to the outcome of the operation.
'Hurrah for Cancer' is a humorous personal take on living with cancer that will add a positive touch to the strand.
Murphy said: "This season is not just aimed at those who may be dealing with cancer personally, it also aims to help and educate all people whose lives are touched by the disease."
Other highlights include artist Tracey Emin's directoral debut 'Top Spot' and Jonathan Ross's 'Memors of a Middle-aged Punk'.
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