here's a bioshock 2 plot which wouldn't have required much retrofitting:
one of the little sisters from the first game grew up and went insane - the topside world hadn't been kind to her, in ways it was crueler than rapture, and that combined with the psychological scarring from having been a litle sister causes her to snap and abandon all reality
she goes back down to rapture, the only place she can still relate to, and eventually finds a way to turn herself into a thinking "big mommy" - maybe it was an abandoned project ryan had started for dealing with little sisters growing up?
she's been surfacing and kidnapping young girls, turning them into little sisters and pairing them with newly created/reactivated big daddies (new enemies! new powers and weapons!) to form a whole "family" she can call her own
she believes in her mind that nothing in rapture is as bad as what happens on the surface, that the girls are better off down there where she can "protect" and train them - only it's evolved into more of a hive situation with her as the queen
tenenbaum found out and returned to rapture with a bunch of other folks to stop it and see if the big mommy could be saved, but of course something went wrong and tenenbaum is the only one left
she finally finds and out of desperation reactivates you - project delta, to rescue the girls, stop the big mommy, and destroy rapture once and for all along the way (explaining why you can't return to areas once you leave)
you have another ally, a male member of the team trapped and hiding at the other end of rapture, who helps to guide you once you reach a certain point (tenenbaum is killed helping you destroy a part of rapture early on and this man takes over her role)
along the way you find recorders and discover what really happened to tenebaum's team of scientist rescuers - they've been turned into big mommy's "workers," the mini bosses you fight at the end of each level, warped and corrupted by adam into serving her, creating new forms of splicers (drones), adapting some of the little sisters into warriors defending the hive (big sisters you fight along the way), and new gene powers have also evolved from their work
you are given the choice of "saving" or "harvesting" these mutated scientists as you defeat them - harvesting gives you fucktons of a mutated adam you can use to permanently infuse your weapons/ammo, "saving" gives you a normal amount adam to spend on gene powers (if you save them they'll help you fight for a while, but they all eventually die either way)
this also gives you a real reason for rescuing every one of the little sisters other than your own morality, and if you harvest them the game would actually get tougher, more big sisters and splicers sent your way by queen big mommy as extra punishment for harming her children
big mommy would talk to and taunt you along the way, sometimes popping up to fight you herself until you could damage her enough to make her retreat for repairs
the twist? bioshock has to have a twist, right? well, how about two - you'd find out towards the end of the game that the little sister who grew into the big mommy was your real-life daughter before you were turned
project delta was taking real-life fathers and daughters and making them into big daddy/little sister pairings - the physical and emotional ties were supposed to result in more efficient and productive adam gathering, but there weren't enough pairs bonded by blood to make the project sustainable and the results weren't any better, so you were thought to have been discarded
twist number two - the man you had been talking to the whole time was the big mommy all along, her personality had split, and the other personality was formed by what she had remembered of you before the turn - for all intents and purposes you've been helped by, and guided by a version of yourself
see, deep inside she knew what she was doing was wrong, she knows that her mind is fucked up beyond all repair, and what she really wants is for you to just kill her and let her go - you're pretty much gonna have to kill your own daughter
(endings after you've destroyed rapture)
"good" ending: you saved all the little sisters and scientists, and let the big mommy die in the collapse. You've escaped via sub, so you deliver the girls back to their real homes and then are taken care of by a couple of the sisters from the first game (who'd finally made it down to rapture to help you out a bit towards the end) - it's a short and melancholy life, though, because even though you are treated well and loved you were badly damaged during the escape, and you spend your time grieving over an old picture of you and your daughter she gave you before she died.
"bad" ending: you harvested all the little sisters and scientists. you pulled the damaged big mommy into the escape vessel at the last second - now you are standing on top of the surfaced vessel with the big mommy, staring at the city shoreline on the horizon. through the window of the vessel's capsule you can see crates of stored adam and syringes. you're about to spread the word of rapture and the glories of adam to the surface world and "save" humanity.
"ambiguous" ending 1: you saved the little sisters but harvested the scientists, and
let the big mommy die. you and the sisters stand on the deck of the vessel staring at the city, and when the camera swings around you see all the sister's eyes are glowing. "look at all that adam, daddy," one of them says, and you see a glow coming off the city skyline.
"ambiguous" ending 2: you harvested one or more of either the sisters or scientists, and pulled the big mommy into the escape vessel. you both stand on the vessel, and she tells you that she knows now that even the best of humanity can be tempted by corruption at times, but now that you're together again you'll both be able to lean on each other and get through it. the camera sweeps across the water and we see a section of rapture drifting in the water. on it are a bunch of splicers, several crates of adam, and syringes. most of the splicers are down on their knees and appear to be praying to an inactive big daddy propped against a broken wall. one of the splicers stands next to the big daddy, holding forth like a preacher and gibbering about a phoenix rising from the ashes. he mutters something about only needing a child to lead them. in the distance we see a cruise ship headed towards the floating wreckage.
anyway, that's about an hour of my life i'll never get back.
