Ok... Try this. An idea I've had since the first Hurt pic was released and only reinforced - not contradicted by various rumours and spoilers since.
First thought - the GI was resurrected for a purpose this year. The G.I has sought to possess The Doctor's body as a vessel - and his knowledge- before - Web of Fear?.
The GI attempts to fuse with or "jump into" and posses The Doctor at the point of McGann's regeneration. Result: a "carrier" 9th Doctor. Not a villain strictly speaking but certainly The Doctor an unwilling vessel of the GI. He may fight this possession during the course of the 50th, or be totally consumed (I favour the former). What chaos would this cause?. What crimes he'd rather forget would The Doctor commit?. Ultimately it will be Clara that saves The Doctor - that's possibly also been foreshadowed for reasons I'll come to.
The 50th is resolved by The Doctor regenerating to the "true 9th" Doctor and the obsessives can relax that their numbering system is intact still - though The Doctor has still "lost" another regenerative process (on top of that Tennant hand business... Such an idea stands up to a certain amount of foreshadowing in series 7. Now a lot of other fans have picked up on certain stories referencing "Alien" this year. "Cold War" obviously as "Thing from Another World" was an inspiration for "Alien". Also "Journey to the Centre of the Tardis" for it's production design. There have been many other observations made such as the "Hide" creature. Now I'm not a big fan of that film but I was pondering one or two ideas so I did some research. Indulge me while I throw in a few more possible nods:
Mr Sweet had a certain similarity to a certain chest bursting Critter. Who was the "innocent victim" and carrier of Alien infection and incursion in this film?. John Hurt.
Perhaps, just perhaps a mischievous Moffat has been foreshadowing the 50th with a series of thematic clues rather than a traditional story arc this year - tucked away in most episodes for those who like to hunt. Interestingly, the flashback in "Crimson" aped another classic British film: "The Elephant Man" starring....
I believe someone has also pointed out a Transformer toy that is perhaps too rare to just be a prop?. Hints at reincarnation of an existing character and would fit in with pop culture references foreshadowing the themes and plot to come.
We also have a young audience introduced and educated to the ideas of The Doctor being susceptible to infection (Crimson) and split regenerative personalities (Silver).
Older viewers are of course used to both concepts.
Ok, if you buy all this tosh this lets consider Clara... To all intents and purposes she's" Ripley" in my proposed analogy (played by Sigourney Weaver in Alien). This places the Companion at the heart of the story of the mystery of "The Doctor" - just as first set out in 1963 (not just a Nu Who invention!).
In Alien Ripley had a fraught relationship with the Ship's computer - sound familiar?.
In Alien there were two "heroes" - Ripley and her newly adopted Ship's Cat. What was TARDIS compared to this year, and what "magical" animal is referenced in the fictional children's book by Amy recently released online?...
(TARDIS as a cat was a nice nod to the Cat's Cradle book btw!!)
The Companion and the TARDIS are The Doctor's salvation.
A lot of fans have obsessed over Clara's preference for wearing red. Interestingly, Sigourney's other big film role of the period was "Working Girl" where she played "The Boss". Many of the most well known stills show Sigourney in red. The film is perhaps most famous for it's hit song "Lady in Red...
Maybe a case of seeing patterns... or maybe just maybe a series arc of cultural nods foreshadowing the finale and 50th. Clara fails to totally resolve matters in the series finale setting up the 50th. Essentially a two parter really.
You decide if I'm bonkers. In my defence Id say just look at how much imagery is consciously being used in "Silver" referencing old Cybermen stories - not to mention little nods to all eras throughout the series. Imagery as a shorthand for themes is very big this year.
PS Back on Gallifrey Base two years ago I suggested a fitting 50th would be the appearance of a "wrong" First Doctor. Setting up the opportunity for a one off appearance by a big star in a revised history of our Character's earliest days as he and Matt have to set the timeline right. Not only could Moffat milk pathos with the inevitable death of this Doctor never meant to be, but any canonical changes to our understanding of established lore would be argued over for years by fans as top whether they remain valid if the timeline was changed. Plenty of opportunity for mischief.
I discounted my own idea at the time as perhaps risking being unfairly criticized as too like The Next Doctor in some ways. As things are looking - was I roughly on the right lines with my suggestions?.
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