Well, this isn't the most complete write-up I've seen, but I got lazy :/. (and tired of cherry picking through my email logs 8). I think I've left out a number of other optional events as well, but... Anyway, without further ado

...
The basic idea for the storyline of the module hasn't really changed much from JBG's original ideas as best as I understood them. Warsong and I have expanded upon these ideas, as well as lifted some ideas that Warsong really liked from my Lunacy post. Roughly, the story outline go like this...
Era: (O = optional/R = Required, # = option category; Two options in the same category are either/or) Description.
Era 0 is before the game starts and represent prehistory for the mod. Optional events only are considered to have "occured" if the player selects that option in the Map Options when generating the map.
0: The first experimental colonies are put on the Moon by China and the US, these are glorified research stations which pave the way for full scale colonization attempts at the start of era 1.
0

O) After the first wave of research outposts, an attempt is made at establishing a robotic colony. After 20 years of success, contact with the colony is lost, as in Sci-Fi glory, some AI takes control of the colony and severs contact (possibly with some interaction with solar storm events). This paves the way for the existance of robotic barbarians and robotic colonies in era 1.
Era 1 is dubbed Exploitation. The main purpose of colonies in this era is to rape the Moon for whatever resources and projects are most valuable to each factions parent organization on Earth. Era 1 colonies will be (little more then) excuses to take advantage of the best squares available in the game. Era 1 will also involve posturing for access to and control of precious water (and other valuable resources)
1: Plans are finally given life simultaneously by various earth groups to colonize and exploit the moon for long-term human habitation. Research groups as well as a variety of private companies and associated groups of privileged individuals put their plans in action and establish sustainable independent populations of colonists on the Moon. This starts the colonization of the Moon scenario. The "justification" for the coincidental timing of these colony foundings is somewhat hand wavey, but is based on mutual knowledge of other groups intent to go, and the need to wait until after the last 11*11 solar storm (giving players 120 turns to prepare for the next one).
1

?) The UN. One thing which Warsong and I have bumped into quite a bit during our fleshing out of techs and likely progression of colonization of the earth, is that, at the point where one can send materials to and from the Earth, and one is inclined to conflict militarily with other colonies on the moon, it is trivial to do so via ICBM type rockets. Although a domestic nuclear program would require a lot of infrastructure build up (and some tech to go along with it), conventional missiles would be easily manageable. We've had a lot of discussions about how to mitigate these factors, and one currently popular for eras 1-2 is the idea of some form of UN agreement banning the use of missiles or nucleonics on the moon. I don't have that discussion in front of me, but I expect we'll include it in the design draft.
Era 2 is called either Colonization or Adaptation. Colonists will have been on the moon long enough to have developed theories and gained access to real adaptation techonologies. This is a bit of a misnomer because I also talk about adaptation techs in terms of adapting existing terrestrial technologies to work on the moon, but.. let's ignore that for now. Era 2 Colonies will begin to have real options, and the tech tree wil start to have optional branches. Distance should impose enough risks that the idea of marching "an army" should not be an attractive option. Conflict should be possibly only between relatively closely-spaced colonies.
Era 3 is the Age of Survival. Cut-off from the Earth, the colonies are forced to fend for themselves. Who has prepared themselves the best to survive the harsh realities devoid of safety nets presented by human habitation of the Moon. Era 3 will start out with some decline, with the loss of food supplies and a need to research new techs to make expansion more likely. Era 3 will also begin to show the first serious advantages to stronger players, as available space becomes more scarce, and as adaptation begins to "shrink the moon"
3: Isolation. The precise event (and therein certain nuances of the nature of the isolation) as well as the timing are chosen by the player at the start of the scenario. The nature of the Isolation event impacts not just the speed of the separation, but also the introduction of odd events on the moon, and the nature of Era 5.
3

R-Isolation) Nuclear War
3

R-Isolation) Zombie Plague
3

R-Isolation) Regular Plague
3

R-Isolation) Global Warming
3

R-Isolation) World War III (Conventional)
Era 4 is the Age of Expansion, and represents the first serious conflict age in our minds. With some player turtling in preparation for Era 5 and others using their higher adapatation ratings to consider launching attacks against other players. Era 4 is when we might expect to see the first plausible military victories (player-caused exterminations).
4

O) Lunacy. If selected, there will be an ideological plague that will spread through the moon involving extreme genetic manipulation of animals and then people to better adapt to the Moon, leading to paradigmal shifts in philosophies, values and outlooks which in sum total are dubbed Lunacy. In a game where Lunacy takes root, the player has the choice either to embrace Lunacy or fight it. Lunacy will involve its own specialized tech tree with some pretty sci-fi oriented techs. It is as close as we are currently intending to having anything like "aliens" in the mod.
4-5

O) Doomsday Cult. With the isolation of the Moon a fatalistic ideology sparks up which, if allowed to take root, can lead to a colony rebelling and attempting to build an all Moon culture destroying device. This is a particular pet event of Warsongs, but we have a better description of it then I'm giving here. The map setting only allows for the introduction of the ideology. It is required to be allowed to spread and take root for it to advance to the stage of actually being attempted. Obviously, if a colony rebels and starts this project, all the AIs will attempt to prevent it from succeeding.
Era 5 is the Era of Reassertion. Earth emerges from its.. whatever.. and attempts to reassert its influence over the moon. Based on why contact was lost, the Earth basically does a Colonization style attempt to retake the Moon, by influence if possible and by force if necessary. Their forces depend in part of the difficulty of the game, the number of turns, the reason for loss of contact, and the scores of all the Lunar factions. The idea being that banding together in preparation for reassertion works, but not as well as it would if Reassertion was a flat force. Factions on the Moon are given a choice to ameliorate the Earth (pay tribute to buy more time), capitulate (doesn't lose you the game but does cost you *alot* of victory points), or refuse. Factions which successfully declared independence before loss of contact are in an advantageous position for Reassertion. Factions which have embraced Lunacy are automatically targetted by all terrestrial factions which remain. I am debating making the Reassertion era also optional. Also there are a number of ideologies which come into play with the reassertion of Earth.
6: Sovereignty
7: Dominance
8: Diaspora
These are still sketchy at this point, but the basic idea is that in 6 you have the final playing out of true independent nations not on some sort of emergency footing, but real sovereign nations dealing with each other in a much analagous fashion as due those on Earth.
Dominance is really just like regular civilization with Wonder races, offensive and defensive tech racing and the ever present need to expand and succeed.
Diaspora refers to the development of independent space programs and the ability to colonize Mars or other solar systems. This is where the space race victory equivalent would be.
By the by it is currently only our intention to flesh out the first 3-5 eras and see how we like the feel of the new ideas, then expand from there. The farther we get from current technology the more flexibility we have to make the game "however we like it", and the less real world knowledge we are behooved to keep in mind.