When we last met our Bioshock hero, he was on his way towards the last two levels of the game.
Spoilers : Show ▼
The “good” ending to the game (it’s relatively common knowledge that there are two) opens up the suggestion of a bright future. It reinforces something that you sense as constantly lingering throughout the entire game: family.
Bioshock is really a game about family. Stephen Totilo over at Kotaku wrote a piece entitled The Daddening of Video Games, demonstrating that quite a few recent games have placed the player in the role of paternal protagonist. Bioshock drives this theme of family more strongly than may be at first obvious. As you pick through the remnants of Rapture, there are little things that pop out, many of them much more subtle than the obvious inter-relation between Big Daddy and Little Sister. In fact, I could write quite a long list of them, but I might save it for another article.
And so, I have finished Bioshock.
A quick review of the trophies shows a few missing — I didn’t fully research the Bouncer or Little Sisters; I didn’t fully upgrade more than four weapons — but, with the way the story ended, I do not feel as bothered by this as I thought I might.
And with this done, I look over on my shelf and see that I must still return to Rapture at some point: Bioshock 2 awaits.

If you're interested, there's actually three endings. The extra ending is visually identical to the “bad” ending, but is narrated differently.
[Reply]
Oh good point. I was just thinking of the visuals and forgot about the narration.
[Reply]
http://www.geekosystem.com/batman-bioshock/
[Reply]