(Minor spoilers for Bioshock Infinite)
I've been playing Bioshock Infinite recently (a couple months after release). The game is beautiful and disturbing and has pretty good gameplay. I'd recommend it to any fan of FPS games. (Heck, I'd have enjoyed it as a purely exploratory non-combat game, given how interesting the opening levels of the game were. Their society based on religious worship of the United States founding fathers is fascinatingly disturbing in and of itself, and that's before you add in racism, a prophetic leader, odd super-science and gorgeous 1900's visuals.)
One of the really good elements within the game is Elizabeth, who is both the goal of the game and combat support. Her character is that of a highly intelligent and powerful innocent who is suddenly exploring the world for the first time. It is literally a joy to watch her experience even simple pleasures for the first time.
I've been seriously considering including Elizabeth (and maybe Rosalind Lutece, the super-scientist who made the floating cities possible) in the Alpha series, but I finally realized that the earliest they could come in would be Chapter 4 (though 5 or 6 is more realistic). Bringing them in would be exceedingly easy, plotwise, since they can both jump between dimensions (and apparently time as well). Bringing in multiple Elizabeths would be just as easy, since by the end of the game it is apparent that there are possibly infinite versions of her.
(As a side note, to those fans of Alyx Vance of Half-life 2, who I consider to be the other great female FPS sidekick, I've always planned to bring her to life, but not until a specific future story/setting.)
So my aborted start to that story took up a lot of the past couple weeks. Now I'm back on track with the current Alpha stories.
The spread of computer intelligences is going to have world-wide impacts. (Heck, a government will be toppled in chapter 2 in what amounts to a large side-note.) This is a 'genie out of the bottle' scenario.
Balancing those aspects of the story with the character stuff is proving to be challenging, and some of it is going to develop in little asides or excerpts throughout the chapters. Chapter 3 will see the first full-chapter focus on the larger stage story.