Once upon a time, a woman named Amy Pond had her newborn baby girl kidnapped by a shadowy group of time travelers known as the Silence. They used trace elements of the vortex in the baby's DNA and stolen knowledge to manipulate her genetics into an approximation of a half Time Lord. The manipulation afforded a certain hardiness, a knack for time travel, enhanced reflexes and intellect, and should have given her the ability to regenerate and two hearts. Their imperfect knowledge, however, left her with still only one, and an imperfect ability to regenerate. When mortally wounded she could still heal all of her wounds with a flood of energy, but it wasn't as efficient and all-encompassing as a real regeneration, and instead of rebuilding a new body it simply healed what was already there. No new faces for their little assassin.
For the first seven years of her life the child, Melody Pond, was raised in an abandoned orphanage, psychologically tormented and scarred by the creatures of the Silence, tampering with her memories, erasing and rewriting them over and over again, feeding and playing with her fears to keep her broken and malleable. When the time came for her to be moved, however, terrified child called for help. When the help that came for her was no less terrifying than the orphanage itself, the child took matters into her own hands and ran.
She didn't stop running until she couldn't any longer, sick and dying of exposure in New York City. When the fire of regeneration cleared from her vision, a strange man stood in front of her. The Doctor, who she'd learned to fear and hate, and who she immediately attacked. As attacks from hysterical and regeneration-sick seven years old tend to be, however, she wasn't very effective. Once she stopped to listen, this strange, sad man with the ancient eyes and infinite fondness seemed to know everything about her, and not just her past but her future. He offered to take her away from the monsters and she ran with him to see the stars.
Young Melody Pond traveled with the ancient Doctor for five years in the TARDIS, learning to pilot the TARDIS under his direction (with a certain knack for it thanks to her genetics) and even learning the dialect of his people. He taught her about the universe and time as well, laying down the laws and the loopholes and what can and can't be tampered with as he took her across the stars and back. Some of her favorite times would be when he'd tell her stories about her brave and clever parents, who he used to travel with long ago, but no matter how many times she would ask, he would just change the subject without answering.
When she was twelve, the Doctor taught her the most important lesson: that all must eventually come to an end. He left her in a cozy home in the 51st century with a house full of things, her childhood diary, the sewn patch her mother used to carry (given to her on her eighth birthday), and a promise she'd see him again.
Despite the look in his eyes, see him again she did, except without the memory of the five years she'd just spent with him, and this time it was only one quick adventure and home again. Over the next three years she learned their new score: their timelines would never really synch again, sometimes running backward and sometimes jumping around randomly (although never did she see a Doctor who traveled with her for five years.). The jumbled timeline could have been frustrating or could have even inspired despair in her, but instead it became a game. The first and most important rule of the game was always lie. Rather than acknowledge the danger of a jumble timeline, or the reality of what that would eventually mean, they used the 'gaps' in their memories to construct elaborate lies about 'spoilers', and competed to find out who could make the most ridiculous lies and still get the other one to believe them.
When she was fifteen she met a darker and more run down Doctor than she'd ever seen before. On her adventure with him, she finally learned of her parents' fate: The Doctor said that her father had been murdered in a selfish, petty, pointless act, and in her grief her mother had demanded to be let home, unable to explore the stars any longer without him.
The Doctor stopped appearing after that. At first she was surprised and confused, and then she waited dutifully...and then her patience wore out. She stepped out on her own without the Doctor. She dyed her hair, originally ginger-tinted, then fading to the sandy brown of her father, to bright blonde to differentiate herself from the child who depended on the Doctor, and sought out a life made by her own hand. Of course, having spent her entire life time traveling, with the beckoning of the Vortex in her mind courtesy of her Time Lord DNA, even the 51st century held no interest for her. At first she became an archaeologist in the hopes of capturing the wonder of time travel without the aid of a TARDIS. When, after getting her doctorate, that didn't work, she used the knowledge the Doctor imparted to her and her own knack for time travel to construct the vortex manipulator. It wasn't as accurate or nearly as safe as the TARDIS, but it worked to go back and see the things she studied for herself.
As time went on, she became embittered to the Doctor's sudden disappearance from her life, and her adventures in the past became more grand scale. Eventually continuing to work on her own wasn't feasible, but rather than follow in the footsteps of the Doctor and take on one person, promise them the world and drop them off suddenly, she chose to go the much more efficient route of establishing an entire agency full of suitable 51st century time travelers. When the time came that her Agency, already gathering notoriety and infamy from is theft of artifacts and law breaking, needed a name for its head...Melody turned to the badly translated patch her mother used to carry. choosing to reverse the name so it wasn't such a blatant swap out, Melody Pond became Doctor River Song, chief of the Time Agency.
The brutal reputation it garnered wasn't by her own dictation so much as the lack of concern she had for controlling or even filtering the people she chose to work for her, should they have useful skills. Without even realizing it, she'd created for herself an organization not all that unlike the one who originally kidnapped her as an infant.
At about the age of twenty-five, she was atop the universe, living without care or consequences, and rapidly without morals. The lessons the Doctor taught her about morality were forgotten, and the Silence's weapon was left behind, wrecking havoc on the universe for the Doctor to scramble and solve rather than the Silence's machinations. Eventually, Doctor Song received an anonymous tip about a bit of ancient technology, supposedly from a race of beings long extinct and nigh-mythological, capable of fixing her vortex manipulators and making them as accurate as any TARDIS.
Of course River Song personally went to retrieve it, wearing 51st century armor which, while obscuring her lovely figure and face, would thoroughly protect her from any defenses the overzealous planet might have implemented to protect their 'sacred artifact'. Everything went according to plan until she had the artifact in actually her hands. She'd missed one last alarm, and thus alerted the place to her presence. Her hurried escape was interrupted by an annoying tourist-looking man, who refused to move and insisted that the loss of the artifact would destabilize the atmosphere and kill everyone on the planet. Rather than be slowed down and potentially caught, she shot him.
When the strange woman immediately ran in from an adjoining room, River nearly shot her, too, just to be done with it...until she heard the name the woman screamed...and saw the Doctor standing off in the distance, expression horrified.
His last story to her crashed in around her, and sudden realization dawned. These were Rory Williams and Amy Pond...and she was the petty, selfish woman who murdered her own father for a useless artifact. She removed her helmet to apologize or speak, but she could find no words. When security arrived, she offered no resistance, and neither her mother nor the Doctor offered protest. She made no attempt at escape, nor at concealing her identity. When Galactic police caught wind of her arrest they immediately swooped in and took her to serve for the murder of Rory and the assorted crimes of the Time Agency in Stormcage.
She vowed from then on to become the sort of woman her parents would be proud of, even if she could only do that from behind Stormcage's bars. The first action, once she learned of who gave her the anonymous tip--and that it had been meant for her to kill the Doctor in her haste rather than Rory--was to escape for a brief jaunt to the Silence, and turned their weapon against them.
Of course that was only the first escape, because suddenly the Doctor started showing up again. Early on it went half and half between her familiar Doctor and the reverse timeline, long enough for her to realize her childhood infatuation had blossomed into love...and long enough for her to realize those feelings weren't returned. As time went on, the out-of-synch appearances of the Doctor waned and disappeared.
Eventually the Doctor started showing up with her parents in tow, and the game they played became one-sided. Seeing her parents alive and happy was overshadowed by watching the Doctor slowly slip away from close friendship and endless trust to suspicion and distance, as he eventually even 'forgot' who she was entirely, and then...stopped.
For awhile she was alone in Stormcage again, as she waited for their first meetings, and then everything changed. When she started seeing the Doctor again it was once more out of synch and randomized, and the vitality of their game was recharged. She earned a pardon, and after the last time she saw her mother, she studied to become a professor. She ended up married to the Doctor about five more times (Atop the three before), and at some point ended up the target of a malfunctioning psychokinetic weapon, which ended up with her getting a good chunk of his young academy life in her memories, including his name.
She teased him mercilessly about it.
She didn't even expect it when the day came that he stared at her blankly. At first she couldn't believe it, and then she took refuge in their game, even if it was one sided again.
Eventually Melody Pond discovered the answer to why they'd always played the game, why their life was so tangled up, and what she'd always been meant to do. She'd been born to kill the Doctor, but ultimately, despite Madame Kovarian's best efforts, she'd lived to save him. She gladly embraced her fate and her lifetime.