5. The Daleks Masterplan - 9/12 Episodes Missing (Plus 1 Prologue Episode)
At the time, this was ambitious. It had been in planning for a very long time and it featured the Dalek's at their most evil, joining forces with various galactic leaders to take over everything, using a super weapon that could age planets to death. Mission to the Unknown was the first episode to not feature any of the regulars and instead featured Dalek's being very evil and putting their plans in place, as observed by a couple of James Bond-like figures from the future. A few weeks later, when the true story kicked in, the Doctor has to stop the Daleks and it takes him a full twelve episodes and the deaths of two companions to do so. This story is unique and it is such a shame that such a large proportion of it is missing, including Doctor Who's first ever 'Christmas special', The Feast of Steven.