Ok I'm a Whedon-o-phile. Deal with it.
In this story instead of Mal and his crew reaching Miranda and successfully exposing its secret, we're going to veer off topic a little. At some point in the original narrative, the Operative manages to snatch River and here's why.
Once he sees River in action he begins to question whether executing her is the right decision. Yes, she's undoubtedly suffering from minor brain damage and trauma but despite all that she remains a formidable force, a one woman army. She's a genius, she just needs to be handled a little more carefully.
He finds the strength of her bond with her brother interesting and potentially useful. The Operative puts it to his superiors that with a little more tinkering by the 'hands of blue' River can be made more stable. At the same time, he wants total seclusion with her. River is psychic and he is a terrible man who has done terrible things and regrets none of them. She'll see the attack on Haven that obliterated the place and she'll see how satisfied with it he was. All she'll get out of his head are reasons to fear him, because he is the man who doesn't ask why; he just follows orders in the most ruthlessly efficient way possible.
Once she fully comprehends what and who she's dealing with, he can really go to work on her. He can test every trigger she has and even give her new ones. Psychologically he will get into her head and kick things around until she comprehends the kind of malice she's dealing with. He wants her demoralised and doubting herself, as well as her sainted big brother. The real thrust of his new mission though will be to get her unquestioning obedience by any means necessary because the Operative intends to become her full time handler. If River can be kept on a short enough leash to become more asset than threat, she could wind up being the greatest Operative of all time.
The Operative is a pragmatic man who knows that despite the fact he's a vital, if unpalatable, part of the Alliance's bold vision for the future, no Operative has lived to old age or been pensioned off onto a nice core world to live out their remaining days in peace. He also knows he's not getting any younger and that the day he fails in a mission it will be his death sentence. Black Ops are a young man's game and keen new faces are always rising through the ranks, hungry for glory that they'll never publicly receive. He's counting numbered days.
Naturally, once River is mission ready the first thing she's going to destroy is her brother, swiftly followed by the rest of Serenity's crew. The self loathing that will inevitably cause in the calm after the storm will be something he can work with. She has to lose faith in herself before she'll put it in him.
The Operative's superiors agree to the plan but they think it's a reckless gamble with little chance of long term success. Early indicators of River's potential were off every chart however and they will take a chance on the Operative in order not to lose that. They want all this carried out on the most isolated rock they can still communicate with regularly, so after the scientists are done with her, River and the Operative get a moon with a view. It's been terra formed with the absolute basics and that's it. The only tech will be on the Operative's lab ship. There is nowhere for her to run unless she steals it and leaves him there. The lab ship has been modified to contain her but River can think her way out of anything.
Naturally she spends much of her time there trying to kill him and escape. They wind up playing cat and mouse across a fairly temperate rural landscape. He's forced to outthink a mad genius and she's forced to butt heads with a kind of absolute sociopathic determination she's not really equipped to deal with.
When he's forced to physically restrain her, a teenage girl (18+ obvs) his little psychic gets more insights she's not prepared for, namely what the Operative finds himself wanting to do to this pretty little weapon of mass destruction. It's been a long while since the Operative was troubled by such appetites. He knew he couldn't forge a specialist career in such a trusted position as lone operative, without turning his back firmly on his misspent youth. River's highly fluctuating vulnerability and her slight build just bring the predator roaring out of him, however. He's secluded with the power of life or death over her. If she can't be worked with, he'll kill her and leave her to rot on that moon. He's not going to admit failure unless he absolutely has to, of course.
The Operative tries to limit himself to psychological sadism, mockery and corrosion of River's self worth/confidence. The Operative is one of the few people single minded and skilled enough at compartmentalisation to be able to lie to River. When he's forced to chase her down through dense woodland however, River falls victim to a savage, truly primal rape. After that he decides that the simplest way to get her obedience may be as primal and unevolved as good, old fashioned subjugation. What he's not prepared for is how suffering at the hands of blue has unwittingly rewired River into the kind of creature that can 'enjoy' sexual, physical and psychological masochism.