Nearly every fan has a theory on how Steven Moffat will pen his way out of this, the rest are just completely (and understandably) confused. We've had a scour through the forums to collate your expectations on season five's final episode; here are the most popular theories...
Dream Lord Interference
Earlier this season (in episode seven to be precise) some psychic pollen infiltrated the TARDIS. It gave The Doctor and his companions, Amy and Rory, two visions: one of them freezing to death in the time machine, the other of the couple's home life in Leadworth--where they were expecting their first child, but threatened by pensioner-inhabiting aliens.
The Dream Lord claimed only one of the worlds was real and Amy had to decide which one. Though it turned out both were "dreams" the penultimate episode revealed that recent events have been formed uniquely by Amy Pond's imagination. She's clearly important as The Doctor has hinted: "what's so special about you?" But how can this be? It is possible the Dream Lord's pollen is still clogging Amy's airwaves.
Angelfishsolo: "Dreams have been mentioned on a few occasions as well. My guess is that reality is not quite real at the moment and Amy will hold the answers (the fact she appears to have died is irrelevant IMHO)."
Agreed. When Rory died in an Amy's Choice vision his existence continued in real-life and in the other "dream". Meanwhile, the hallucination in which he seemingly died continued without him. Not all of it could be in Amy's head though -- for one she's never met a Cyberman before.
River is The Doctor
How else can she drive the TARDIS? The Daleks have said that only the Doctor can pilot it.
Copygeek: "That would explain the diary she has (since a couple of previous Doctors have been shown to keep diaries), how she is able to pilot the TARDIS so well, and how she has the sonic screwdriver. Also, it would explain how she knows The Doctor's real name. It COULD even explain how she is responsible for "killing" The Doctor (which has been implied, but not explicitly stated I don't think) if she were to be The Doctor's last regeneration. Her death would result in the death of The Doctor."
That pretty much covers that topic, doesn't it? Only problem is… how is this possible? We saw David Tennant regenerate into Matt Smith, not Alex Kingston. She could be a Doctor from the future, but that wouldn't explain all of her back story. Nor would it explain the sonic screwdriver--he gave it to her. Besides, even Amy knows how to function some parts of the TARDIS. Chances are the Daleks are misguided, as are we.
Wallross001: "And we saw Donna have a bit of a go at flying the TARDIS during the Sontaran Stratagem... If River was the Doctor, then there'd be a fair bit of time continuum stuff going wrong whenever they'd meet."
Time Can Be Re-Written
We've seen it happen before this season: Amy and Rory saw older versions of themselves across a lake in The Hungry Earth, but after Rory died in Cold Blood elderly Amy was re-seen alone. The Tenth Doctor's reign bore witness to a similar pattern in The Waters of Mars too. Perhaps these were just tastes of things to come? It does feel like a bit of a copout.
Althalus69: "The Doctor is imprisoned in 102AD, the TARDIS explodes 26.06.2012... What will probably happen: Young Amy Pond will find the Pandorica (way before 2012), open it, the Doctor is set free and will stop the TARDIS from exploding by foiling the Alliance's plan."
It is certainly possible. If that is the case River Song will no doubt be a driving factor in the change, seeing she's trapped in a different time and desperate to continue fighting.
Amy is the Key
Amy Pond grew up in a home surrounded by perception filters and cracks in time. That has to make her somewhat special. Just think: of all the gardens to crash into the TARDIS crashed into hers, twice.
Though she's dead she's not been erased from existence (like Rory was) and now River is back in her house, which is full of young Amelia's toys. This suggests (as do preview pictures) that Amelia will be able to help out where her older (now seemingly deceased) self cannot.
As Angelfishsolo points out: "In the first episode the doctor states: "I am a mad man in a box, remember that; it might save your life one day"."
We'll find how the finale concludes this Saturday, June 26, from 6.05pm on BBC One. Do you have any theories to add?