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1 - Arrival
As the elevator rises up to his lair, Fontaine comes across your shortwave radio with one last message for you. "I remember when me and the Kraut put you in that sub. You were no more than two. You were my ace in the hole, but you were also the closest thing I ever had to a son. And that's why this hurts. Betrayal, kid. Life ain't strictly business."
It's really a shame that the developers never added the option for you to take Fontaine up on the deal he offered to you earlier. But, alas, this fight is inevitable.
2 - Fontaine
You arrive to discover that Fontaine has strapped himself into some sort of Adam-injecting machine, and has obviously been using it to juice himself up with a massive dose of Adam. He's no longer the timid-looking mobster type you saw earlier. Instead, he's now a giant of a man with hardened, gray skin pulled tightly over rippling muscle tissue. All of his hair has fallen out, making him look more like an alien than a human. And a badass alien, at that.
You're in no immediate danger upon your arrival, so don't do anything to him just yet. Have a look around his lair to make sure you know where the Health station and Gene Bank are, just in case you need them. As scary as Fontaine might look, he has no power without his Adam. When ready, hit him with the ADAM Harvesting Tool to drain a quarter of the Adam coursing through his body. This will prompt him to knock you back twenty feet and the fight will begin.
During your first bout, Fontaine assumes a fire-based form. Along with the fireballs he tosses out, Fontaine uses his extreme quickness and agility to charge you with his right shoulder, after which he'll throw a left uppercut that will stun you for a few moments if it hits. To avoid this nasty combination, ready up your Winter Blast 3 plasmid and use it freeze him in place while you put some distance between the two of you. Personally, I like firing the crossbow at him once he thaws, but launching a Frag Grenade or Heat-Seeking RPG would do the trick as well. When his health is reduced to zero, he'll teleport back into the Adam-injecting machine. Move quickly up to the machine and impale the bastard once again with the Harvesting Tool to drain another quarter of his Adam.
For the second bout, Fontaine assumes a cold-based form and calls in some security bots to annoy the hell out of you during the battle. Make a run for the Bot Shutdown Panel directly north of his machine and deactivate the bots before you suffer too much damage. Fontaine is completely immune to your Winter Blast 3 plasmid in his new form, so ready something else up instead. Telekinesis combined with the explosive barrels stacked at the back of his lair make a very potent weapon, for example. Whatever you do, just make sure you're strafing to avoid the stream of ice shards he launches across the ground at you. Getting struck by these will freeze you in place for a period of time while you continue to take damage from Fontaine's other attacks. Keep hitting him with the explosive barrels or your standard weapons until he teleports back to the machine and you can drain yet another quarter of his Adam.
Fontaine's body crackles with electricity during the third and final bout, granting him the ability to quickly launch purple and black balls of lightning at you. Some damn Splicers have joined the fray too, so you'll probably want to hit them with Enrage or lure them all to the back pool of water for some Electro Bolt action. Fontaine is susceptible to your Winter Blast 3 plasmid again, so you can use the same tactics this time as you did the first time around. As long as you wipe out the Splicers right away and are able to move out of the way of Fontaine's balls of lightning and crushing shoulder lunges, you shouldn't have too much trouble sending him back to the injection machine. Hit him with the Harvesting Tool one last time.
Although his Adam is completely gone, Fontaine still has the strength to leap from his machine in an attempt to keep fighting. Before he can lay another hand on you, though, Little Sisters begin leaping out of the nearby vents and start stabbing him with their harvesting needles. Shortly thereafter, Fontaine lies dead.
What happens next depends on whether or not you chose to harvest or rescue the Little Sisters during your time here in Rapture. I don't want to spoil the final cinematic, but let me just say that there's no way to achieve a "neutral" ending. You're either the orphans' savior or a sadistic bastard. Both cinematics are rewarding in their own way, I suppose, and give you at least some sense of completion. Until next time, Jack. Congratulations on finishing BioShock!