Update: Ken Levine has contacted Shacknews to clarify that the player in the prior revision of BioShock's story did not necessarily reprogram a lesbian character; such actions are merely examples of the sort of tasks actual deprogrammers are hired to perform in the real world. Irrational's earlier story was more political in nature, with a deprogrammer being hired by a senator.
Original story: BioShock's creative director Ken Levine detailed the bizarre former premise to Shacknews during an extensive interview about BioShock, its world, and its fascinating and deranged denizens. The interview is packed with spoilers, however, so here are his remarks presented in a safe setting:
"There was another story before that about a cult deprogrammer," Levine explained. "I don't know if you know what a cult deprogrammer is; it's someone who goes to take people out of cults to deprogram them so they no longer believe in it. It's a weird thing, because they're basically kidnapping people."
The game's protagonist was one such fellow. "[There are] people who hired people to [for example] deprogram their daughter who had been in a lesbian relationship," he continued. "They kidnap her and reprogram her, and it was a really dark person, and that was the [kind of] character that you were. It went through a lot of changes. That wasn't really fleshed out, we just needed something, and I said, 'Maybe I'll develop this, maybe I won't.'"
It may seem almost unbelievable that a game could undergo such drastic changes, but Levine emphasized that the development principle at Irrational Games (now 2K Boston and 2K Australia) has always put design first. "A lot of the game design elements stayed the same," he said. "Story changed radically, but gameplay always comes first for us."