The Eleventh Doctor faced his worst fear in "The God Complex," which was revealed to be the ever-present crack in time, but is there more to this Doctor Who mystery? In Doctor Who season 6, Matt Smith's Doctor, accompanied by Karen Gillan's Amy Pond and Arthur Darvill as Rory, is whisked into a simulated reality that takes the form of a hotel. Each room in the hotel harbors the worst fears of a specific guest; Amy's, for example, contains her younger self waiting endlessly for the "raggedy man" to return. The Doctor opens his own door (No. 11, naturally) and, with a wry smile, mutters "of course... who else?"
"The God Complex" itself doesn't reveal what lies in The Doctor's room, and fans had to wait until season 7's Christmas special to find out the answer. "The Time of the Doctor" shows that the hotel room contained the crack in time that followed the Eleventh Doctor around for his entire run - the crack that was ultimately confirmed to be the Time Lords of Gallifrey reaching out to The Doctor, hoping for a return into the universe. However, this explanation comes with a few problems. Firstly, Matt Smith's character clearly says "who else" after opening the door, suggesting a person was inside. Secondly, The Doctor didn't yet understand the full significance of the crack in time. And, lastly, with centuries of constant misadventure to pick from, why would The Doctor's greatest fear be something that he first encountered just one season ago?
The hotel in "The God Complex" seems to manifest a person's greatest fears, rather than focusing on one specific phobia, so the crack in The Doctor's room could have been accompanied by a person. Someone like the War Doctor. Played by John Hurt, this secret regeneration was The Doctor's greatest shame, and he went so far as to drop the "Doctor" title during this lifetime. Nevertheless, The Doctor committed horrific acts during the Time War, and prior to the 50th anniversary special, believed he had wiped out both his own race and the Daleks in one final attack. If would make total sense if the War Doctor was waiting inside Room 11 in "The God Complex." Not only would the "who else?" line fit perfectly, but The Doctor has always been afraid of his own inner darkness, and John Hurt's character was the epitome of that.
The War Doctor and the crack in time both relate to the same fear, so it follows that they'd be together inside Room 11. Before discovering the truth, Eleven was ashamed of his secret regeneration and terrified of repeating those actions. This lingering fear explains the manifestation of the War Doctor. The crack in time, however, proved that the Time Lords were still alive, absolving The Doctor of his sins. Subconsciously, The Doctor knew this because his Tenth regeneration was present at the time, so maybe the hotel simulation plucked the truth from The Doctor's forgotten memories, and showed both his darkness and his salvation.
In reality, The Doctor's door in "The God Complex" is likely another example of the convoluted storylines that dominated Matt Smith's tenure. Recurring elements such as River Song, The Doctor's name, The Silence and, indeed, the mysterious crack were all changed, rewritten and retconned as the seasons passed. Some fans claim that the crack is visibly reflected in Smith's eye as he peers into Room 11, but the true intention of "The God Complex" was arguably always keep the contents of The Doctor's room a secret, before an explanation was squeezed into Smith's final episode for the sake of completion.