Marco Polo - S1-E4
Trivia: This, the fourth Doctor Who story, is one that did not survive the BBC's purging of the archives in 1972-78. Originally seven episodes were made, and first broadcast in February-April 1964: none survive in the BBC's archives, and the entire story is one that is "missing believed wiped"
Answer: It was never destroyed on-screen; it was intact at the end of the TV movie, and destroyed by the start of the 2005 series. It was destroyed in the novel "The Ancestor Cell," but in a completely different manner to what happened in the series.
DaveJB