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Frequently Asked Questions                                {c13}
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1. Why did Atlas/Fontaine go through all the trouble of deceiving Jack?

The first, more obvious answer is that it's easier to get someone to do something if they believe in it and are motivated to achieve that goal. Instead of risking an insubordinate Jack fighting him every step of the way, Atlas wove a believable story to make Jack personally hate Ryan, and thus motivate him to kill him.

The second reason is that Atlas was simultaneously tricking Andrew Ryan, who he knew was listening into all of their radio communications. Ryan did not figure out that Atlas was actually Fontaine, and that Jack was actually his son, until moments before Jack reached him. If Ryan had known these things earlier, things would have played out much differently. Ryan could have exposed Atlas as Jack's slave driver, or refrained from blowing up the submarine if he knew that there was nobody inside.

2. Who blew up the submarine in Smuggler's Hideout?

Ryan did, thinking Atlas' family was really inside.

3. What do those tattoos on Jack's wrists represent?

The chain tattoos on Jack's wrists symbolize his role as a slave. Fontaine created Jack for the sole purpose of carrying out his wishes, so it was the entire embodiment of his existance.

4. Is Ryan really dead?

Yes, Ryan is dead. There is a Vita-Chamber in a hidden corner of his office, but it is the only one in the game that is de-activated. Ryan shut it off before the confrontation with Jack to prove a point, and leave the world on his own terms.

5. Why did Fontaine have to use Andrew Ryan's son as his assassin?

The fact that Jack is Ryan's son is the sole reason he is able to travel freely throughout Rapture using the Rapture Metro bathysphere system. Ryan had Sullivan lock down the bathyspheres during the war, and only those closely related to Ryan and his inner circle could come and go as they pleased.

It is also the reason why Jack is invincible in Rapture; he is able to use Ryan's Vita-Chambers, which are genetically locked to Ryan himself. This is why the splicers in Rapture die permanently while Jack can ressurect. An assassin that cannot die is the perfect assassin.

I'd also like to comment that this is absolute brilliance on the game developers' part; that such an integral part of the story explains the player death/resurrect mechanic perfectly.

6. I seem to have thought that the Little Sisters-as-scavengers predated the
  Atlas/Ryan war. Weren't they already being cultivated for this purpose by Fontaine for his Adam industry?

The Little Sisters were adapted to become scavengers only after the war began (after Fontaine had become Atlas and Ryan took over Fontaine Futuristics), when corpses began filling the streets and they realized there was Adam to be had. Something important to note is that Fontaine got all of his Little Sisters strictly through the orphanage. These were little girls with no families, etc. Ryan, on the other hand, got them all through kidnapping, which is ironic considering Ryan is the leader of Rapture and Fontaine is a notorious crime boss. All of the kidnappings you hear of in the audio diaries are directly linked to Ryan Industries. The Little Sisters before Ryan (for example, in all of Tenenbaum's recordings) are just "Adam factories"; there's never a mention of them physically going out to do any harvesting.

7. How do you know that Sullivan killed himself?

It is never directly stated in the game that Sullivan killed himself, although it is heavily implied. Sullivan was a good guy at heart who followed orders from a corrupt official and ended up doing some very horrible things, including killing a guy during interrogation and a singer for writing a few songs that upset Ryan. After he killed Anna Culpepper, the audio diary talks about how he took from her room a half-knitted blanket after killing her as a reminder of what he'd done. It's clear that at this point he is very remorseful and on the brink of quitting. When Ryan finally enacted the death penalty by hanging, Sullivan handed in his badge. We never hear from him again, and there is a dead body in the wharfmaster's office next to the interrogation room and the "Have My Badge" audio diary. We can therefore reasonably conclude that Sullivan committed suicide for the atrocities he committed during the latest parts of his career as chief of Andrew Ryan's police..