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We know she'll end up there because:

she kills a very good man.

I really don't want to think it's the Doctor, but it does cross my mind all the time. She won't tell the Doctor, so it's a very, very good man they both know.

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We don't know. Unless you spend some time in spoiler-specialized Doctor Who forum where you'll find possible reasons, we won't know until either the summer break or worse, the end of series 6. –  Loïc Wolff May 17 '11 at 9:07
    
I don't think it was the Doctor - she killed a GOOD man, and he's either great, horrible, FANTASTIC!, frightening, or whimsical. He's a veritable force of myth and nature, not a man. –  Jeff May 17 '11 at 12:16
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The Doctor is killed in 2011, at the picnic, so it wouldn't make sense if River had killed him there and is in prison in the 52nd century (or so -- don't remember her exact year). –  Tango May 17 '11 at 17:49
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I'm tempted to say that River ends up in prison because the Doctor keeps taking her back there - but I wont. –  Lekarz Kto May 28 '11 at 14:11
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She kills John Goodman. –  StuperUser Aug 15 '11 at 17:04
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8 Answers

In the events of "Let's Kill Hitler", we find out one of the fixed points in time is...

River killing The Doctor.

Now, it's still possible, based upon details in the Rebel Flesh, that the Doctor that was killed could be a 'ganger instead of the real one. Of course, which one is the real one?

It has been indicated the Doctor has a limited number of regenerations, Is it true that The Doctor (BBC's Doctor Who) can only regenerate 12 times?, so it could be that they plan on letting the Doctor pass on at some point in the future anyways, with Matt Smith. The Doctor who dies is in Matt Smith's incarnation, so I would lead towards the 'ganger - so the real Matt Smith can retire in the future and they can figure out a way around those 12 regenerations for him.

River had regenerations at one point, but she passed them on to save The Doctor. Otherwise, she could always take on the story.

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i did think of the same thing - river staying there just because she's willing to, thats what makes me think how good that man must be –  dzambaska May 17 '11 at 12:44
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The opener for Season Six doesn't necessarily confirm or deny that River didn't kill the Doctor. –  Keen May 17 '11 at 13:40
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@Keen - excellent point. We have no idea who was in the suit at that point in time. We know the young girl was in it in 1969, but we have no idea who was in it after that point. –  BBlake May 17 '11 at 14:25
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It's possible there wasn't anyone in the space suit either. However, I think the lightning isn't very in character for River. I find it unlikely it was her. It is interesting to speculate though! –  Travis May 17 '11 at 14:49
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Don't forget, by the time of the incident at the lake, the River watching the Doctor's death has already (in her timeline) committed the crime that got her put in jail. If it was her, she would have known it was going to happen, but she clearly didn't. –  Daniel Roseman May 18 '11 at 9:08
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This is because of the event in The Wedding of River Song (series 6 finale), and was further explained in First Night, a mini-episodes produced exclusively for the Doctor Who: The Complete Sixth Series DVD and Blu-ray box sets.

River has been apprehended, taken to the 52nd century and incarcerated in the Stormcage Containment Facility to serve twelve thousand consecutive life sentences for killing the Doctor.

But also note that

She served the sentence only to make the Silence believe the doctor is dead.

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12,000 consecutive life sentences?! Call me soft on crime, but that seems a bit excessive for killing one person. –  Keen Apr 27 '12 at 15:36
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As the doctor is the last time lord, killing him is, in fact, genocide. 12000 life sentences is probably reasonable for that. –  Sean McMillan Sep 7 '12 at 18:38
    
The Doctor saves billions of lives about every couple of weeks, and the entire universe every couple of years. When you consider the consequent risk to everyone if he dies, 12,000 is too cheap. –  Tynam Dec 26 '12 at 11:20
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I still think it could be River in the suit. Surprised or not, it still would be shocking for River to watch herself kill the doctor as a witness from the other side especially if she knows she is in the suit and why she killed him in the first place. She also then tries to shoot the astronaut to no avail and we all have seen that she is a crack shot!
Either way I love the character and I can't wait to see it unfold. I hope I am wrong and that River is NOT in the suit!

And for that matter River NOT Rory tries to stop Amy from interfering while they are running to try to save the doctor. Rory is Amy's gladiator and would lay down his life to make sure she is safe. I would have thought he would have bee the one slowing her first? Far fetched but just a subtle thought.

Lastly, what was up with the "newer" model Jeeps the agents used to track down Amy and the gang? Was that real time running in 1969. I thought it was just three months after Amy shot the little girl? I must have missed the time jump... Must watch again! Cheers!

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On the fact that River shot at the astronaut and misses - when she misses, she says, "Of course not". Post "A Good Man Goes to War", it occurred to me that if Melody (Young River) is in the suit, then River could not kill Melody because that would create a paradox (which cannot exist w/o a bastardized TARDIS at its heart, of course...). Thus it would be metaphysically impossible for River to succeed in killing her younger self. –  The Evil Greebo Jun 20 '11 at 16:59
    
@reese, there were numerous "mistakes" that were overlooked in the 1969 episode. First, there were few black secret service agents with such high placement at that time. Second, the secret service in 1969 phased out revolvers. And if you really want to get picky, the tape recorder in the prequel wasn't exactly the model used by the president at the time, although it was similar. And you want to get picky because they couldn't find vintage jeeps? –  David Good Sep 5 '11 at 22:32
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Officially, it's because she killed "a very good man".

When you consider how often she breaks out of the prison, it's clear that this is largely a self-imposed punishment.

During A Good Man Goes To War, Rory catches up with River just as she's on the phone with someone at the prison, telling them that she's breaking in, not out. The alarms then turn off, and you never see a guard in the scene (as she walks back to her cell). Apparently her coming and going is neither noteworthy or concerning.

If I was funnier, I'd say it must be because the rent is cheap or the view is good. It's certainly not because she must be there.

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I'm pretty sure she kills the Doctor which lands her in such a "high security" Prison. Why else would she be there? She killed a good man... Everything clearly states that she kills him.

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I'm not convinced she's in prison BECAUSE she "killed a good man."

In Time of the Angels the Bishop says "you're the only one who can manage him - that's why you're here. But it only works as long as he doesn't know what you are."

Also, the Bishop says the Doctor shouldn't trust River because she kills someone - I don't remember for sure, but I'm thinking he only implies she's in prison because she killed someone.

My theory is that the clerics put her in Stormcage so they could use her to manage the doctor whenever they felt the need. Clearly killing him wouldn't prevent his meddling, since he's a time traveler.

I also think she stays in jail because she promised the doctor she would (she says "I have a promise to keep.") - clearly it's not really any kind of problem for her to get out. Maybe the doctor wants her there so he can easily find her.

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It is entirely possible that the 'good man' who is going to war and the 'good man' that she kills (as she does say she is in prison for killing a good man) could infact be Rory, especially as during the begining of 'A Good Man Goes to War' Amy tells Melody all about Rory and makes him sound incredibly heroic (something very much supported by his dealings with the Cybermen!)

Also, the doctor states he is not a good man, good men don't need rules, and "today is not the day to find out why I need so many"

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Do you think she would kill her father? –  dzambaska Aug 12 '11 at 12:01
    
@dzambaska It certainly would explain why River was so regretful of it when she spoke of it. –  Keen Aug 12 '11 at 14:09
    
I thought this was going to be the case. As we now know, of course, the Good Man was the Doctor after all. Shame. –  Daniel Roseman Oct 3 '11 at 9:53
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It has not been revealed in the story yet, so everything is speculation.

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