I need some advice on a story I'm doing right now, it's a development going in the background of the game, which may have an impact on the player characters. Here's the story:

There is a former cop, nothing fancy or special. He has some investigation skills, some fighting ability, but nothing that would make him top tier at his field. At some point he get to be on the wrong side of the truck driven by cruel fate and ends up in a hospital without any limbs and with a few hours to live without life support for which he has no money to pay. At this point some smiling and very polite people appear in his ward an offer him a chance to live, which will need an extensive implantation (which he can't afford, but the generous gentlemen offer him a credit). Being drugged and clearly not in his mind, he agrees to their proposal. Some time later he leaves the hospital, perfectly healthy with new implants that boost him to the limit of his physical metahuman capacity, a shiny skillrig and owning a substantial sum of money to a corporation that took interest in him.

Now, how can a said corporation return their investment? I understand that if such a situation arose, no sane corporation would offer to spend money without knowing in advance how they would profit from it, but let's imagine in this case they had some other, non-profit concerns, and getting the money back is optional, but a highly desired option. The implants made the victim a capable fighter, but as I said, he is not top-tier. Still, it's his strongest point. So, how can his benefactors profit from it, assuming they want to get their money back fast and then start actually profiting? I thought along the lines of bounty hunting, but it's a rather slim line of income.

You've just written the standard Street Samurai background story. The corpers get their money back by having someone whose skills they know they need under their thumb and with every reason to do the job they want him to do. Even a full-body job is petty cash to a megacorp, after all.

Could be they want someone who knows police procedure, and can blend in with them, to act as a private investigator who will have to interface with the cops a lot. Could be they want him for infiltrating Lone Star or Knight Errant. Lots of possibilities.

How fast will a street sam return investment? I imagine they don't get that much money

"Oh, you don't have the money for this week's installment? Well, you're in luck. It just so happens that one of our competitors has let it slip that they're working a new model of drone that we'd like to get our hands on. Prototype and blueprints, or we'll start thinking about the cranial bomb."

It doesn't sound like something a corp would do , if they want a cybered up thug they can just use existing employes "Bad news Bob your position has been made redundant, but we do have an exiting new opportunity for you! or you get no unemployment and you kid gets pulled out of corp school." on the other hand it does sound like the kind of thing a Fixer or mob boss might do.

1. Some runner team sells you some used cyber cheap
2. Dr Bob owes you a couple grand from when you bailed him out with his bookie
3. That Cop you tried to bribe that one time is dieing in the ER

1+2+3 = A pet thug with the street smarts and police knowledge to avoid trouble, no match for a real street sam or adept but he's good enough to scare off any civilian or ganger short of an Ancient or Halloweener. as long as his records are clean use him as a bodyguard or security for short terms no questions asked work that reputable agents wont take. As he starts do get a shadowy rep transition him into leg braking and other criminal work. Take 50% off the top every job and it will pay off fast, offer higher paying jobs if he gets new cyber with "low" interest loans.

David Sarif did it, so it's a thing a corp might do. Not AAA probably

Character gets 2 cranial bombs, a kink for control and an area for containment, an internal comlink, a Headsafe and a cyberware backdoor (RC106) in addition to the other ware he got. The Happy Smiley Man and co. explains that the player is now the bearer of some very important confidential information that they would rather not chance falling into the wrong hands and since the player has no connection with the group s/he was the perfect coincidental choice.

If he steps out of line, micro bomb turns him into a vegetable and the comlink transmits his location to HSM&co so they can come pick up their 'ware to stick in someone else. If he or someone else tries to access the info, the area bomb takes out everything (ditto for trying to remove any of the 'ware or if the character flat-lines). Occasionally they contact him through the com-link (hopefully not during a 'run ) to set up a covert meet to sync up the data in his head, or warn him that his current SIN has been compromised.

Eventually things between HSM&co and their adversary degenerate to the point that the character needs to figure out a way to get out from between then or s/he's going to wish for that nice quiet death in the hospital.

Plausible deniability is ALWAYS valuable.

Besides, employees might have families and other pests like that. Grab a random dude from a hospital with the basic skills needed, and no family to speak off, and you got yourself an asset that can't be easily traced back to you, who nobody will miss.

Families etc are the key to control. When someone decides that he's not going to get out of this alive when keeps him from shooting you in the face? Fear of being killed? He's already decided he's going to die, he's just trying to increase the size of his honor guard in hell.

But they also ask annoying questions such as "where did my daddy go?" and make silly demands like "explain again why I shouldn't report my husband missing, giving Lone Star access to the tracking software in his commlink."

I'm behind this kind of logic, a big corp wouldn't risk an investment like that to pesky details like free will. Especially not when you have free reins to chip him up to become the employee of the month.
If it were for a potential CZ subject, an investment like this would make sense. It's not like people are lining up as volunteers for those kind of projects.
On the other hand there is plenty of filthy rich "eccentric" people that would very much entertain such an idea, heck some of them with mostly altruistic motives.

He's on a business trip. And his paycheck gets deposited in their bank account every other week.

So here's where I come down after much deliberation: The megacorp element of the Shadowrun universe is distinctly cyberpunk and as such bears the burden of that genre's cynical tradition. The megacorp can't have anything other than sordid intentions for a nobody saved from the jaws of death and conspicuously rewired for combat (read suicide mission with very specific necessary skillset because of his skillwire. Something like underwater welding in a school of sea monsters.) however if you need your character to remain alive for and participate in several or many runs, it seems plausible that said evilcorp is conditioning your character's relationship to his handlers and testing his responses to high pressure situations. Equally plausible that corp is simply waiting for their dastardly global chess pieces to align for maximum evil. Either way, ultimate outlook for your character is not good in my professional opinion because even if he miraculously gets through the suicide mission alive, evilcorp will still insist it is owed for the wares--and thus a second suicide mission--or will simply off him for deniability (and recover its tech incidentally). You can guess which option I find more likely. Bottom line: corp could have a motivation for keeping him running for smaller margins but you have to accept that it is only a short term arrangement with an absolute albeit floating termination date.

Perhaps gather data for some very specialized knowsofts/skillsofts/etc? "Oh, subject 3X7-00HN1 has broken into the Aztechnology pyramid? Get everything you can for the mapsoft, data on their physical security, perhaps we can ride shotgun on their hacker as well?"

Don't forget the joys of internal rivalries - the wired operative may be one suit's pet project, an experiment in low-cost deniable operatives 'dump some tech and let them learn the hard way, cheaper and less traceable than really *intstructing* someone for that sort of crap or such nasty reasoning. While the guy in the next office will do anything he can to spoke his wheels (and of course while both of them are busy squirelling whatever grey or black cash they can get to feather their own nests and pay for a move to take out their boss and get his seat. While keeping their own underlings from doing the same.

Sure the corporatiosn are nasty toward outsiders - they're just as bad (if not worse) amongst each other, though the rules are somewhat different, tending more toward character assasination and sabotage than physical assasination.

edited for fairly horrible typing

Which ca nlead to all sort of funny things of the 'but I work for the same corp as those guy why are they after me ?' sort

If you have access to a spell check of some sort (various browsers have built in versions, or ones accessible by add-ons), it would quite help legibility on your posts. Making a post more readable generally makes the reader focus more on the point one is trying to get across, whereas one fraught with spelling errors will have them spend some of their attention on that.

Free will can be edited out of the equation with the right mix of Warez.

Skill wires, hardwired implanted comlink with Sim module and a pilot program. And viola! Meat Drone with no say or cognizance that he ever did anything illegal.

I'm assuming he's a former cop at the time of the accident (otherwise that does give you some more hooks).

There are still some possible reasons why. For example:

The corp is showing off their new line of experimental life-saving technology. If the tech doesn't work, they clean up the body and no one is the wiser. If it DOES work, they tout how kind they are, and how great their technology is, everyone is smiles and rainbows that they returned to the community by helping this public servant, etc. Two months later when the hubbub has died down, they kill the guy and reclaim the ware, making their losses negligible.

The corp thinks this guy is a nutso. They implanted their COMPETITOR'S ware, and plan on the PC leaving a swathe of destruction, now forever associated with the competitor's company.

As above, but the ware has been sabotaged. The PC is going to explode messily, showing everyone the competitor's ware sometimes has some unexpected consequences ...

A smaller unit within the corporation, run by an overambitious manager, is planning to show to his superiors how great their recent work is, by taking a nobody, upgrading him, and then throwing challenges at him to prove how effective he is (so the PC's fairy godmother is going to keep sending tougher and tougher challenges until the PC dies, or kills said fairy godmother).

As above, but the manager is hoping to kill the project, by upgrading a decorated and combat-tested officer of the law with this supposedly 'new thing' in ware, then sending some "minor" challenges that snuff out the new robocop.

Dragons! Specifically, one dragon, playing a very long game, to create and equip a team without them realizing who is pulling the strings, and direct that team against the dragon's enemies.

"Alright, all done upgrading John Smith, just like you ordered, boss."
"I said JOE Smith, JOE Smith! Who did you just sink a million nuyen of ware into???"

I like the last one, too bad it never comes true! %)

But in the end the easiest way proved to be the best - fellow was rather capable as a bounty hunter and returned the investment in a couple of runs. But that doesn't leave much for story and plot hooks, he's more like an background npc now rather than a potential player character or focus of a story. I might dig that dragon line though...