Caution: Spoilers Ahead for Doctor Who: Flux
In the anticipated Doctor Who: Flux finale, an exchange between season antagonist Azure and the Doctor finally answered a question posed during Matt Smith’s run as the Eleventh Doctor. Having cornered the Doctor in anticipation of the final Flux event, Azure claimed to be able to see into the Doctor’s mind, as well as her greatest fear. Back in Doctor Who season 6, episode 11, Matt Smith's incarnation of the Doctor also seems to face his greatest fear, though what Eleven really saw was left a mystery to the viewer.
In the episode, entitled "The God Complexx", Matt Smith’s Doctor—along with his companions Amy and Rory—investigate a mysterious hotel stalked by an enigmatic monster. In this hotel, the corridors contain dozens of marked doors which hold visions of an individual person’s greatest fear. One room, notably room number 11, contained the Doctor’s greatest fear, which is never shown on screen in the episode. However, upon seeing his greatest fear, the Doctor stammers: “Of course. Who else?”
In the finale of Flux, however, Azure seemed to provide an answer to this mystery, stating that the Doctor’s greatest fear is “the destruction of other things […] you want to keep things alive.” However, this answer seemingly contradicts what the Eleventh Doctor sees in his room, which is answered (in a way) by the end of Matt Smith’s regeneration. Though not the first time Doctor Who has contradicted something from Matt Smith’s era, in this way, Flux teases a different answer to what the Doctor saw in The God Complex, or at least a different meaning behind what he saw.
In Matt Smith's final Doctor Who episode, "The Time of the Doctor", a memory of the past reveals that the Eleventh Doctor saw a crack in time on the wall within the hotel room. This implied that he feared the ramifications the crack could have on the universe, his companions, and the resurgence of the Last Great Time War. However, in Flux, Azure’s interpretation seems to imply that the Doctor’s fear of the cracks in time represents a more general fear of being unable to defend life.
Alternatively, in keeping with many of Doctor Who: Flux’s confusing retcons, perhaps Azure’s statement about the Doctor’s fears is an attempt to retcon "The Time of the Doctor" and its answer to the question set up in "The God Complex". Over its 6-episode run, Flux has made many attempts to retcon many previously established rules and ideas introduced in earlier seasons. Azure’s answer regarding the Doctor’s greatest fears could be the latest example of this trend.
Though past episodes and seasons have attempted to give longtime fans of the series further insight into the Doctor’s personal history, as seasons change creative hands, these answers seem to be growing increasingly more contradictory. Whittaker’s era of Doctor Who is no exception to this. Indeed there are few similarities that remain between Whittaker and Matt Smith's Doctors, though their greatest fear—depending on how viewers interpret it—could be one that does.