Doctor Who: Every Series Plot Thread Ranked Worst To Best
2. The Woman In The Box
Okay, this might not have been the longest story arc. In fact, it only lasted for less than half a series, but for imagination, twists and impact, it must be regarded as one of the best in history.
Amy Pond was pregnant, yet she wasn't pregnant. At random intervals, a menacing looking woman with an eye patch would look at her through a small slot, that could appear in just about anything. Both mysteries were highly surreal, and seemingly disconnected. The Doctor, being The Doctor, smelled a rat, and took Amy on a supposedly random expedition to a facility occupied by human Flesh clones, who were busy appealing for some rights of their own.
It all appeared fragmented, and the penny didn't drop until the final five minutes of the closing episode. Amy was in fact a flesh clone, and her real pregnant self was trapped in a white box with only the venomous Madame Kovarian for company. It paved the way for the excellent A good Man Goes to War, and by all rights, Doctor Who's storytelling had never been stronger.