During her final month in her pregnancy, River notices strange things with her husband's behavior and confronts him about it. At the same time, she ends up going into labor, leading to the Doctor making a difficult choice, and one that he hoped to never make again.
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For an entire month, the Doctor continued his search for the real River, only for his search to come up with the same message every time: no results. Despite this, he never gave up his search, knowing that the real River—wherever and whenever she was, despite her mind currently occupying a Flesh body that she believed to be her real body—was counting on him to find her, save her, and bring her back home safely.
At one point during the month, even though he didn't expect to find much, he decided to return to Demons Run, because who knew; maybe he would get lucky and find something of use there. The moment he arrived, of course he found nothing; not a single thing that indicated any sign that River was there, nor any sign that the Silence returned to attempt to revive their former base of operations. No surprise, the place was left just as abandoned as how he last left it, after he rescued Amy all those years ago. A small part of him hoped that the Silence had returned to revive their former base with River, as it would've been much easier to save her since he knew the place so well after the last time, but at the same time he didn't think the Silence would be dumb enough to return to a place where his army knew they previously operated and would take over the base again just as easily as last time. No, he thought, the Silence are much cleverer now; of course they would've moved their main base of operations elsewhere—somewhere they would never think for me to look. Of course there were a million bases all over Time and Space, maybe more, and despite knowing that River could be in any one of them, he swore to himself that he would search all of them if he had to or die trying.
Turning his focus back to the present, at this point the Doctor was beginning to sense that his wife was reaching the end of her pregnancy, which was both good and bad—good because she wouldn't have to deal with the pain that typically came with Pregnancy any longer, but bad because in reality she was about to give birth with their worst enemies, the Silence, as witnesses, and once the child was born they would automatically swoop in and do unfathomable things to her; things the Doctor did not want to think about. That's why he wanted to find the real River as soon as possible—so he could stop the Silence from doing whatever it was they were planning to do to his first child in centuries, and he was determined to get there first.
One of the major things the Doctor sensed that was a sign that his wife was, indeed, reaching the end of her pregnancy was the fact that she had been in a lot more pain than she was letting on over the last few days. He could sense through their weak psychic link (it was considered 'weak' on account of River being only part-Time Lord) that she was dealing with menstrual pains that have been becoming more frequent, but whenever the Doctor would ask about the pains, she would just shrug it off as simply being 'Braxton Hicks'—"Just practice contractions," she would say; though the Doctor knew otherwise.
Despite all of this, the Doctor continued his search of the real River in secret from her Flesh self. Since his search has continued to come up empty-handed, he was beginning to think about the worst-case scenario for the reasoning behind this lack of information: he may have to go ahead and 'melt' River's Flesh self, after all. This was something he'd been thinking about for a while, and he was beginning to think that this was the only way to get a proper result. Of course, he didn't want to go about this decision, because the instant he does, he would lose her. Once he melts River's Flesh self, her conscious mind will return to her real body, and only then will the TARDIS find a proper connection, but she would still be lost. He remembered having to do the same exact thing with Amy before he melted her Flesh self, and he hoped that he wouldn't have to go through all of that again, remembering how much it hurt Rory to lose his wife and baby daughter. Of course he found Amy and reunited her with Rory (though it took much time), but they ended up losing their daughter to the Silence, and they didn't reunite with their daughter until she was a fully grown adult, long after the Silence had done what they planned to her (of course this was long before they found out that their childhood best friend was their daughter all along). The Doctor hoped that once he found the real River, he wouldn't be too late to save his daughter as well.
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DOCTOR WHO: Arising -- A Nova Sue Prequel (Part 1.5)
Fanfiction{PREQUEL to my "Odd Life of Nova Sue" series} Not everybody is ready for parenthood, certainly not the Doctor. His wife, River Song, would have thought that her husband would be happy to have the chance of being a father again after many centuries o...