Bioshock may seem like a game with an ordinary story on the surface but it contains a lot of elements that we, today, consider conspiracy.
It tells the tale of man with a great vision for humanity that lead him to create a complete breakaway civilization, named Rapture, under the ocean. A civilization with "no gods and no masters" an anarchical utopia of technological potentiality.
The man is named Andrew Ryan and he was originally from another country, not USA (cultural center around which the game revolves). The player crashes there by accident and is guided through the ruins of this long gone utopia by a man named Atlas who communicates with the player through radio. In the progression of the story Atlas is revealed to be lying to the player about his identity and objectives, actually being a businessman and a smuggler. Rapture much coveted substance, ADAM (that makes Plasmids which give you powers) is extracted from Sea Slugs or young females.
So let's try to unpack all of this information and release what is really being told to the unsuspecting players.
Andrew Ryan is basically a genetic manipulator, he wants people to have superpowers, he's an eugenecist. If you abbreviate his first name and continue with the family name he's A. Ryan, i.e., Aryan. A very clear message is being stated by this not-so-hidden cypher. Andrew Ryan is doing the work of a certain group of people who wanted to improve humanity and take us to a higher ground of being, whether that was done in a good way or not, it's not the main issue here NOW, but let's continue the decoding.
The player arrives at the ruins of Rapture (a rather biblically charged name) by the failure of the technology of his people (plane crash) and is proceeded to be guided through this historical ruin by a man named Atlas. People mistakenly think Atlas, in mythology, holds the Earth on his back, no, that's a misconception: Atlas actually holds the celestial sphere.
Atlas, as in reference to Atlantis, i.e., the material drive to exorcize divinity out of man, leaves man with the burden to carry the whole cosmos on his back. One term used by the dissidents of the West is to call the westerners Atlantists.
Atlas communicates with the player through Radio, constantly telling the player what to do, what to think. Atlas is then revealed to be a businessman and a smuggler, meaning someone who cares only about material wealth and has no morals in pursuing so. Radio is the utmost tool of propaganda, constantly reinforcing a desired dialogue in the minds of the population at large.
ADAM, the coveted substance that made all this wondrous world possible is said to be originally extracted from "sea slugs", if you check the 3D model for the sea slug in the game it looks like an uncircumcised male genitalia from the front and side, but also looks like a female genitalia from the back.
The game also presents the player with the moral dillema of using "little sisters" (young girls). To me the message is quite clear, this is hinting at a process that started from dealing with basic genetic material and this lead to the accidental discovery that if the genetic material is further developed, but not completely, it yields a better results. So, from a genetic manipulation point of view, it's better to use children, for they are like sprouted seeds, more rich in nutrients, but still not depleted after they made the plant grow.
Bioshock, which seems on the surface to be just a highly creative and well written fantastical tale, is actually a very important tale of morality about the hidden technological undercurrents that pervade our current society.
Remember, good art is always the hard truth hidden through beauty.