So  we guessed, did you?
A few thoughts before the second half of the series starts in the autumn – I’m not interested in the “I watched the filming and overheard X” spoilers, more in clues already dropped in the shows and in the official teasing by the crew and cast.

The problem with internet commentary on Doctor Who is that half is from old-Who obsessives that want old characters to link in.  In the past few weeks I’ve read about Omega, the Valeyard, the Rani etc. etc. even though I’ve absolutely no idea who they are really – I was old enough to watch Peter Davison, Colin Baker and Sylvester McCoy’s Doctors in my childhood but most of the mythology stuff seem to be from earlier incarnations.  But I think this might miss the point – the new series doesn’t have to just rely on the past for characters.  For example, when there was a reference to another Timelord in the episode “The Doctor’s Wife”, it was the Corsair – a completely new one!  The much trailed “old friend with a new face” was the TARDIS herself.

Equally some want too strong reinforcement of links to the Eccleston/ Tennant /Russell T Davis era Doctor Who and keep asking for the return of the likes of Captain Jack or Jenny the Doctor’s daughter.  Never mind the filming or family commitments of the actors that played those characters – they are simply not necessary.
Think – Jack enabled the doctor never to fire a gun and has a sucessful spin off series now unconnected to Doctor Who itself.  The Eleventh Doctor has River Song and Rory as weapons-wielders, even Amy shoots guns and flings swords around.
Jenny enabled the Tenth Doctor to talk to Donna about having been a father – which can hardly have been a revelation to the audience (William Hartnell’s Doctor travelled with his grand daughter Susan).  But it is not the Doctor’s daughter but Amy’s that is the focus of the current series’s storyline.  Jenny got to zoom off into space, leaving the door open for a spin-off if the character had been popular enough, or a reappearance if one is ever needed.

Then there are the reviews from people who clearly weren’t listening or watching.
All the stuff about how did he know Madame Vastra the Jack-the-Ripper-eating Silurian who brings a Silurian army on board Demon’s Run to help?  Well, if you watched it, she told us herself – he found her in the underground system of Victorian London taking revenge on the workers for the death of her sisters.  No mystery, but a cool character.
The Stephen Moffatt version of Doctor Who is intelligent TV – the plots are not linear but are always revealed but you need to think about what you’ve seen and there’s plenty to talk about between episodes.

OK, enough of that.  So what are the loose ends?

1) Who is River Song?

• Yep, River Song is Amy and Rory’s daughter.  ”Melody Pond” was a massive clue, and once you threw in the comment from the dying Idris/TARDIS in “The Doctor’s Wife” that “the only water in the forest is the River” it was clear that – linguistically at least – River was going to be something to do with Melody.
• She appears to be the Doctor’s wife too if the kissy kissy faces the Doctor pulled at the revelation are anything to go by.  They have already kissed once from the Doctor’s perspective, and for the last time from hers.
• But what would be written on the cot in untranslatable Galifreyan?  It couldn’t be “Melody Pond/ River Song” – it was old. But hold on – timey wimey wrong order stuff…
  May be names in Galifreyan combine both parents names and she’s the mother of his future children? Or Susan’s mother?
  But equally it could have been the Doctor’s real name, in which case she’d have known it in “Silence in the Library” when she meets the Doctor for her final/ his first time.
  Or she may have known it already if she’s spent a long time with him in the TARDIS?
• She appears to be able to regenerate: how?
  Well, there are still those little hints that she might be the Doctor’s child in some way.  Amy saying to baby Melody that her father is the last of his kind then clarifying she means Rory “the last centurion”, the Doctor answering “because it’s mine” then clarifying he means the Galifreyan cot… And we’ve had build up to the idea that Amy might actually love the Doctor more than Rory – despite the events of “Amy’s Choice” last season where she realises its Rory and always has been.  In “The Impossible Astronaut”, when in the clutches of the Silents, Amy cries for the Doctor specifically – and only possibly for Rory – the “stupid face” stuff is ambiguous and the pay off unconvincing.
  Stephen Moffatt says in Doctor Who Magazine “You’ll see The Doctor’s life change forever. You will gasp at the true nature of his relationship with Amy and cry out in horror as Rory Williams stumbles to the brink of a tragic mistake.”  Given that that relationship at present appears to be him being her son-in-law, I’m not really gasping, so there must be more to come.
  The whole Time Lord DNA thing that the army were looking for in Melody looks a promising strand of confusion and potentially tragedy in the second half of the series.  While this was explained by the “time head”/ mother’s intuition comment that the Doctor referred back to when discussing the DNA issue with his ragtag army friends, where being conceived in the time vortex might have done to Melody’s genes what billions of years did to the race that became Timelords, neither Amy nor Rory were there. Will Rory conclude that Melody is not his?
• The Doctor heads off because he says he knows where Melody/ River is… We know too – she’s in a children’s home taken over by the Silence in 1969, then in a New York alleyway six months later. But there are so many things that are going to happen to her – not least being swallowed by a Silents-made spacesuit, possibly being in the forest and regenerating and possibly killing the Doctor…
• Does River also answer what those sub-TARDISes (in “The Lodger” and in “The Impossible Astronaut/ Day of the Moon”) are for – for her to pilot as an alternative Timelord?

2) How will Silence fall?

• Anyone else think the Silents fell too easily?  Manipulating humankind from the beginning, even organising for the moonlandings so that a spacesuit would be made but vanquished with subliminal messaging during the moonlanding?
• We also don’t know how or why they blew up the TARDIS at the end of Series 5 leading to all worlds collapsing.
• Do Madame Kovarian and the Demon’s Run asteroid army work for the Silents? Building the little girl as a weapon to destroy the famous, great warrior against whom the world must be protected…
• The thing is, we think of the Doctor as a good man, a fun man, a kind man.  And the character is all of those things.
  He is willing to give a chance to the new species he encounters – New Humans created in the New Earth cat-run hospital, the human-timelord-dalek hybrids, the Flesh Gangers he stablisises.  But he is also ready to exterminate the last dalek in Manhattan, the vampire fish (Saturnynians), even the Timelords themselves, for the greater good of the universe.
• Other series of Doctor Who have always had the Doctor able to slip in anywhere unknown and disappear before the consequences of events have to be handled.  This series and the last are different.  Fear of the Doctor – the great warrior able to change the world without spilling a drop of blood, the most dangerous being in the universe against whom an all-worlds alliance formed in “The Pandorica Opens” – the Doctor famous throughout all worlds for nearly a thousand years was a totally different perspective.  It fitted the darker Tenth Doctor from “Waters of Mars”, perhaps less aware of his power but completely unaware of the impact he has.
• It was a neat trick too to have Lorna Bucket – her role was vital in both explaining who River Song is and that the darker doctor, living up to the “oncoming storm”, is a warrior.  It also sets up a forest-based story for the future in which a younger version may feature.

3) Does the Doctor die?

• Killing the Doctor dead, mid-regeneration, gives us the choice of the series ending when Matt Smith leaves, a time reboot (again) or somehow getting a second Doctor.
  As soon as we saw the Flesh, we knew that the Doctor that dies for good in “The Impossible Astronaut” didn’t have to be the real Doctor.
  Of course, the Doctor is at pains to stress that the Flesh Gangers are real – and that the other Doctor is also the Doctor.  Interesting too that Amy trusted the Flesh Doctor more: was it prejudice on her part because of the shoes (which they had swapped)?  Or was it because she was also of the Flesh and there was a familiarity between them from that?
• Does River kill him?  All we could see is the Astronaut that emerges from the lake.  We know that Melody is intended by her kidnappers to become a weapon and brought up to kill the Doctor – and that River is in the Storm Cage for killing “the best man she ever knew”, a good man.
• Is the Doctor a good man? It is clear he’s a just man – think about the Sontaran nurse doing penance for his clone batch and the Family of Blood punishments. But he warns Madame Kovarian that she doesn’t want to see why he sets rules for himself.  The good man, the best man River ever knew is Rory. May be she killed her own father instead.

4) Oh my God, they killed Rory!

On that point, a few thoughts about Rory and Amy.

• Is Rory still an auton?  No.  The Doctor used psychology to make him confront his potential fears, access the determination of 2000 years as a centurion guarding the love of his life (memories there behind a door in his head, he said), and wearing Roman clothes enabled him to go onboard the 12th Cyber fleet.
• Is Rory dead, or going to die?  I think both he and Amy may do so before the series ends at Christmas this year.  Why?  We’ve been prepared many times now for Rory’s death: death-by-old-person, death-by-Silurean, death-by-total-eradication-from-existence, death-by-universe-reboot, death-by-FBI, death-by-old-age-madness, death-by-drowning…
• Amy’s role is also surely almost done – she was an amazing child growing up in a house next to a crack in space and time which in itself could surely have affected Melody’s DNA. Now she’s a mother – and you can’t have a family with a small child on the TARDIS.  But we don’t know how the Silents got the glowing recorder out of Amy’s hand (easier to remove from the Flesh?), how many days she was gone (was that the real Amy with the Silents?) The Doctor says she was taken some time ”before America” – really? Or did he just notice then.

While many commentators have gone on about a gay agenda (the gay, married anglican marines and the silurian and her maidservant being the latest additions to this), far more interesting is the anti-faith agenda.  Think about it: the Headless Monks don’t need a head as their minds cannot be changed and they are heart over head.  And the religious army thing?  Moffat says the national armies of today are the aberration if you look at human history where they have mainly been religious (well, may be) – but more importantly the religious army is both the enemy of the Doctor and guardian of the prison where River is kept (perhaps she kills Rory when he was going to kill the Doctor, hence making her the enemy of the army?).  There’s an episode in the second half of this season called the God Complex.  Can’t wait to see what’s in that as there is apparently a minotaur and David Wailliams as a mole…

While Stephen Moffat’s series of Doctor Who have been criticised as too dark and too complex, I think it is true that the clues are there – they are just delivered so fast and so staccato that it is sometimes hard to catch them on a first viewing.  And that’s the perfect excuse to watch episodes more than once

I’m going to be hugely, embarrassingly wrong about all this in the autumn, aren’t I?