Bioshock > Bioshock Levels > Fontaine's Lair
Make sure you save your settings before you enter the elevator. If you are killed without having saved the game, you will start the game all over again.
As you leave the elevator, you see Fontaine: He is now twice his former size, having become in life the Titan he had been faking for the past couple of years. You see him lying on a gantry with a lot of bottles of Adam pumping into him. After what he has done over the past twelve years, he deserves what you are about to do to him.
The basic plan is to attack him with your Extractor Tool, extracting a fourth of his Adam; fight him until he is forced to teleport back on the gantry; and then attack and extract again. Repeat this until all his Adam is gone.
The catch is that the Adam has given Fontaine plasmatic powers. After the first extraction, he hits you with fire. After the second, he attacks with ice. After the third, he fires bolts of electricity at you.
Then there is Fontaine's backup. At first Fontaine fights you alone. After the second jab, he summons security bots. You can zap them down and hack them to attack Fontaine; or you can shut them down at a bot shutdown station (if you have R$20). After the third jab, aggressors come to fight you. They are a waste of ammo and Eve; so plop them with Enrage to keep them busy, or blow them away with Sonic Blast.
After the fourth jab, you are down on the floor as Fontaine rages:
I had you built. I sent you topside. I called you back, showed you what you was, what you was capable of. Even that life you thought you had — that was something I dreamed up, tattooed inside your head. If you don't call that family, I don't know what is. And now …
At this point Fontaine is overwhelmed by a pack of Little Sisters, who stab him to death with their needles.
The ending cutscene depends on how you treated the Little Sisters.
If you saved all of them, a single bathysphere ascends to the surface. The Little Sisters see the sun for the first time as Jack helps them out of the ship. Then come scenes of the Sisters living normal lives: education, marriage, family. Finally the Sisters hold Jack's hand as he lies dying from old age, probably the end result of Suchong's accelerated aging. Tennenbaum's voice-over implies that Jack had overcome both Ryan and Fontaine and found what both had denied him: A family.
If you harvested any of them, a host of bathyspheres ascend to the surface. They emerge around a nuclear submarine sent to investigate the airplane crash next to the lighthouse. Out of the spheres jump Baby Jane spider splicers, who butcher the crew and take over the ship with its nuclear arsenal. Tennenbaum implies that you have become even worse than either Ryan or Fontaine; and not content with Rapture, you sought control over the secrets of the world.
Regardless of the ending, Suchong's accelerated aging would have killed Jack in a few years. Meanwhile, Tennenbaum left Rapture with the remaining Little Sisters to start a new life on the surface. One of the Sisters could not adapt to such a life; so she returned to Rapture to restore it to its post-war status. To provide Adam for herself and her subjects, she kidnapped little girls from the Atlantic coasts and turned them into Little Sisters. Tennenbaum got wind of this, and reactivated the prototype Big Daddy to stop her and to save the Little Sisters. And so begins Bioshock 2.