This is probably a very rude first post (since I immediately start questioning things), but hear me out here.
While I know "the current story outline is fixed" and as far as I've read that's not a bad thing because it's not a bad storyline, I would like to suggest a few slight adjustments.
The reason for these suggestions is that in the current storyline, humanity either comes out as: a. completely screwed or b. extremely too powerfull in the end.
In the currently set storyline, the enemy is a bio-engineered sentient disease that's hundreds of thousands of years old and that has ravaged our known galaxy for almost this amount of time. Somehow, they never discovered earth (or if they did, they discovered it earlier, but ignored it for not being very interesting and only recently discovered humans living on it now) and now they decide to invade Earth.
However instead of sending their entire armada immediately, they apparently send scout teams (initially) small enough to be defeated on a regular basis (without effort on easy difficulty, with great effort and casualties on the hardest difficulty) by a eight person teams. Then, when the scouts/researchers achieve their goal of being able to infect humans, they still don't send in their entire armada and eventually the humans find a way to blow up the mothership which houses ALL aliens infected with the 'virus' who haven't already been killed or captured on earth.
Now, the fact where I find this to be somewhat unrealistic (and realism in the storyline is one of the things you have made clear is very important to you) is that if this 'virus' has indeed been around for nearly a million years and if it has taken over all of the Milky-way galaxy, then the mothership would have to house literally hundreds of billions of infected aliens and if they don't all reside on the mothership, then the milky-way galaxy should hold hundreds of billions of infected aliens in several dozen colonies.
It seems to me that it would be rather ridiculous for humanity to be able to defeat an alien 'empire' numbering in the hundred billions with a team of 8 (or however many soldiers fit on the PHALANX FTL transport) humans.
Don't worry about being rude, it's fine -- as long as you don't expect your ideas to be adopted without question.
From what I've read of your post, it seems like you've missed a couple of important details in our storyline draft. Let me try to explain point by point.
The 'why not a total invasion' question is self-defeating. Any alien species capable of invading Earth can easily overpower us with a total invasion. That's not the point of the game. Our explanation for the UFO:AI scenario is that the alien mind isn't committing any more resources than it has to to get the job done, which (in the beginning) is harvesting of human material for the re-engineering of XVI to fit humans. That job gets done quite swimmingly regardless of the small-scale interference from PHALANX. At no point in the game are there any real advantages to a total-invasion scenario for the virus -- the drain on its already low resource pool would be terrible. Imagine the cost of trying to manage 8-10 billion prisoners, many of which may be armed. This is a no-go scenario for the virus since it doesn't want to kill all those people, it wants them
alive.
When XVI gets going on Earth, and PHALANX becomes more of a problem, then the virus commits more resources to the field in order to accelerate the takeover. It will be getting some new supplies from mining operations in the asteroid belt and in surrounding systems. Still, anything used on Earth is not being used for the virus's #1 goal, which is to build the wormhole device and leave this spent galaxy for a nice new one. The discovery of Earth was only made in the final mop-up operation covering the last few galactic spiral arms (which is just as likely as any other explanation for an alien discovery of Earth).
Also, the reason why a small team of PHALANX members can blow up the entire alien threat (which is all concentrated in a single mothership, excepting some of the resources on Earth) is because the hive mind can't divide itself. It can't sustain permanent operations more than a few lightyears from the mothership. The mothership is extremely big, yes, with a population of several trillion, but most of the aliens there aren't armed. As long as the team is able to muck up that wormhole device, it'll tear the whole ship apart.
The point of this storyline is also very much tied in with gameplay. We want to keep the player on his toes at all times, strategically on the defensive trying to counter alien plans that are actually effective, and challenged tactically by new weapons and powerful enemies. And of course there's the slow march of XVI, which will be actually unstoppable -- the player can slow down XVI through his efforts, but it will always keep growing until the player is forced to take on the final mission as a desperate action in the face of defeat. (This has been one of our plot guidelines, we don't want to be able to keep playing indefinitely such as in X-COM.)
We've been working on this storyline for a long time, but there are still details left to be fleshed out and a lot of the actual text left to be written. We wanted to bring back some real cosmic horror, and that means humanity standing alone in the face of an enemy of overwhelming power -- but an enemy that
can be defeated against all odds through cleverness, ingenuity and skill.
It also has some other important advantages:
1) No other aliens in the galaxy to possibly appeal to for help. This is something to be very much avoided; if it's possible and you fail to include it in-game, the player will feel cheated. This is a point that your proposal has trouble with, you're forced to handwave why the aliens won't help humanity -- and you end up with a bad cliche.
2) No other planets to mine for handy resources that Earth doesn't have very much of.
3) A consistent set of goals, reasoning and capabilities for the virus, with a long-term plan that is only slowly revealed to the player.
If we were to change the story now, the proposal would have to be very well-written, original, and tight as a drum with regards to plot holes. I'm afraid that yours gets sunk by a couple of fundamental flaws, and the way you present the enemy doesn't really have the
feel that we're going for with this game.
We'll be happy to hear any other ideas you've got, though.
Regards,
Winter