Replying to: Beginning by madmatg
Throughout 1959, a full-scale decline of Rapture took place, with many large battles occurring between the armies of Andrew Ryan and Atlas. Ryan used the opportunity of the conflict to test many of Ryan Industries' plasmids and gene tonics on citizens on the field through Sinclair Solutions, a company owned by Augustus Sinclair. Early 1959 also saw great advances in the technology of Big Daddies under Gil Alexander's influence.
As Rapture society began to fall apart Andrew Ryan attempted to maintain control by enacting harsher laws, limiting the movement of the population, locking dissenters up in Apollo Square, shutting down the Bathysphere network, and putting the death penalty in place for anyone who broke these laws. In an act of desperation Ryan even violated the greatest virtue he held dear, free will, by introducing a type of "pheromone" into the air which would allow him slight mental control over all of the splicers. Once Ryan had complete control of the city, Atlas went into hiding, and the insane splicers roamed the streets of Rapture.
 1960: Jack Arrives in Rapture (BioShock)
Jack, a passenger on a commercial air craft flying over the middle of the Atlantic Ocean, reads a letter attached to a gift from home that begins "Dear Jack, Would you kindly not open until..." (with the rest of the letter obstructed, it is later revealed the whole content of the letter during Andrew Ryan's speech at his office. It says: "To Jack, with love from Mom & Dad. Would you kindly not open until 63Â° 2Â° N, 29Â° 55Â° W"). The plane mysteriously crashes, and Jack "awakes" from a kind of blackout to find himself underwater. He is surrounded by sinking debris from the crash, as well as lost belongings from the passengers. As Jack surfaces, he swims for the only structure in sight: a lighthouse shining brightly among the dark night sky and ocean. It serves as the above-surface entry point into Rapture, a grand underwater metropolis.
 Welcome to Rapture and the Introduction to the City
After Jack enters the lighthouse he descends into the ocean city using a Bathysphere, as the history of Rapture is told through a prerecorded film narrative by Andrew Ryan, the city's founder. Upon arrival, a man awaits Jack's exit from the bathysphere, but is killed by a grotesque figure that is apparently insane. A man calling himself Atlas comes in over a shortwave radio inside the bathysphere, asking Jack "Would you kindly pick up that shortwave radio?" Atlas also informs Jack that he wants to keep him alive. After Jack leaves the bathysphere and moves to safety, Atlas reveals that he has been cut off from his family by splicers; mutated citizens of Rapture that have gone insane and answer to Andrew Ryan. Atlas believes that Jack is his only hope in reuniting with his wife and child, and tells Jack to find his way into Neptune's Bounty where his family is secretly waiting in a submarine.
Jack explores the way into Rapture with the guidance of Atlas until he discovers a Gatherer's Garden vending machine containing hypodermic needles. When Jack injects himself with one, Atlas tells Jack that his genetic code is being rewritten, and in a spasm of pain, Jack falls from a ledge and is knocked unconscious. After awakening, Jack continues on through the city, learning about the various traps, enemies, and resources, until he is discovered by Andrew Ryan, who communicates with the player over a television. Ryan believes that Jack is either an agent of the KGB or CIA, and he boasts to Jack of being invulnerable to the government influences of the Union of Soviet Socialist Republics and the United States of America. The entrance to Neptune's Bounty is sealed off by a security alert, and Atlas tells Jack of an alternative route through the Medical Pavilion.
 Medical Pavilion and the Security Lock down
Jack escapes Ryan's henchmen to Rapture's medical complex, the Medical Pavilion, and continues to learn about Rapture and encounter its inhabitants. Throughout the game, Jack picks up Audio Diaries that reveal small pieces of the plot by themselves, but clear up significant mysteries when considered in full context. Throughout his journey through Rapture, Jack encounters various sorts of Splicers. Jack also experiences brief moments of psychic hallucinations in which he can see ghostly figures walking about, talking, and interacting with each other. According to public address announcements throughout the city, these hallucinations are a side effect of gene splicing oneself.
Through various recordings and hallucinations, Jack learns of Dr. Yi Suchong (a doctor whose involvement with plasmids, as well as his true role in the story, is revealed later) and Dr. J.S. Steinman (a plastic surgeon who unlocked ADAM's cosmetic potential). Atlas informs Jack that Steinman has lost his sense of reality due to over-splicing, and is in pursuit of enforcing cosmetic perfection at any cost. In order for Jack to proceed, Steinman must be killed, as he has the key to override the security lock down, which will enable Jack access to the bathysphere to Neptune's Bounty.
When Steinman is killed and the key is taken, Jack encounters a short battle on the way to override the security lock down. A few Splicers are fighting a Big Daddy. The Big Daddy is finally killed by a large explosion, and a single Splicer is cornering the now unguarded Little Sister. Before Jack can intervene, Dr. Brigid Tenenbaum bursts upon the scene, and dispatches the Splicer with her pistol.
Seeing that Jack is not a crazed Splicer, she informs him that she was heavily involved with the design of the Little Sisters, and that the Little Sisters possess ADAM. But regretful of what she has done, Tenenbaum tells Jack that he should have mercy on them, as they are still young girls. Atlas chimes in over the radio, telling Jack that he needs ADAM in order to survive Rapture, as it will make him stronger. Atlas says that the Sisters are no longer human girls, but monsters; the clear choice is to kill the Little Sister to obtain all the ADAM she has. Tenenbaum once again advises, saying that if Jack must have ADAM, there is an alternative choice to killing the Little Sister: using a plasmid that will safely remove the sea slug. This will spare the girl's life, but only yield half the amount of ADAM she has. As further incentive, Tenenbaum offers future gifts that will compensate Jack for the ADAM he loses in saving the girls. Caught between the opposing counsel of Atlas and Tenenbaum, Jack is faced with a choice.Once he has decided he is allowed to buy Plasmids and tonics from the Gatherers Garden.Then Atlas tasks him with killing a Big Daddy all by himself
 Neptune's Bounty and the Smuggler's Hideout
From the bathysphere, Jack arrives at Neptune's Bounty, Rapture's main dock and fishery. Atlas tells Jack to make his way down to Fontaine Fisheries, where he meets Peach Wilkins. Even with the word of Atlas, Wilkins refuses Jack passage to the Fisheries; he believes Jack may be an agent of Frank Fontaine sent to kill him for his disloyalty. Regardless of the news around Rapture, he does not believe Fontaine was killed, and thinks he is still alive. Wilkins eventually agrees to allow Jack passage based on one condition: Jack must bring him photos of Spider Splicers taken with a special biological Research Camera.
As Jack explores Neptune's Bounty and takes the required photos, he learns through audio recordings about the discovery of ADAM, how Frank Fontaine founded a smuggling ring which funded Tenenbaum and ADAM research later on, how Fontaine's dominance over the ADAM market has changed Rapture's social structure, how Andrew Ryan and Sullivan tried to bust the smuggling ring, and how Peach Wilkins began his involvement in smuggling for Fontaine, though he was torn between taking sides in order to save himself. Jack returns with the required photos, and Wilkins allows him access to the Fisheries as long as he gives up his weapons. Once Jack enters unarmed without conventional weapons, Wilkins and his Splicer smugglers ambush Jack, as he still believes him to be an agent of Fontaine. Through clever use of his plasmids, Jack defeats Wilkins and his smugglers, and recovers the weapons that were taken from him.
After killing Wilkins, Atlas informs Jack that he is very close to the Smuggler's Hideout, where his family remains locked in a submarine, cut off by Ryan's Splicers. Exploring Fontaine Fisheries, Jack discovers the hidden pathway to the hideout. Ryan informs him over the shortwave radio not to help Atlas, or he will learn what it means to truly be his enemy. Jack arrives at the control room overlooking the dock with the submarine, and activates a switch that allows Atlas to arrive at the dock as well. As Atlas approaches the submarine, Ryan's Splicers begin swarming the dock area. Ryan's voice comes over the radio and taunts Jack, telling him that Atlas and his family will be killed, while he helplessly remains locked in the control room. Atlas, using his pistol, fights off the Splicers long enough to escape. But Ryan triggers explosives that destroy the submarine. Infuriated at Ryan's sadistic decision to destroy his family, Atlas tells Jack to get out and get to Arcadia.
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