I think I know a few good ideas for making the story go "off the rails"
1st Idea: Random Order of gamesSince the aliens seem to be Aquatic in origin, what if when you begin as X-Com, you start seeing TFTD enemies instead of the original UFO Defense ones? You could have made choices in Phase one that could lead to the CFN to fund for Underwater combat against aliens rather than Surface combat. That way you either start with either a UFO game or TFTD game, and then after the Alien City/Cydonia falls, it sends a message to the other planet and then you go on to the next game, resulting in a varying metagame experience!
2nd Idea: Defensive endgame rather than Offensive endgameWhat If you would rather not invade Cydonia? After 2 or 2 1/2 years, maybe an alien Super-UFO will be developed, probably using the human face on Cydonia as the hull (Andross!?
) and have enough firepower to destroy the planet! At that point you will have a time limit until the Super-UFO reaches earth to intercept it with an avenger and blow a large enough hole in the hull to invade the ship and disable it. As opposed to stopping all surface alien activity when you destroy Cydonia, you will still have a few (albeit less intense) encounters with aliens as you transition your research to TFTD-related gameplay.
I gotta think of more, but it's midnight here and I should be in bed. Expect more possibly tomorrow.
EDIT: It's not tomorrow but hey, I got more ideas.
3rd Idea: Apocalypse intervenes earlyDuring the land incursion, it is entirely possible that suddenly the interdimensional aliens appear. They could either help the aliens defeat you or become a third party, battling both your XCOM forces and the first alien group. There can be missions where both groups appear and fight eachother, called "Conflict zones." Just think: Mutons vs Anthropods!
The above has a rare chance of happening, but it allows for even more story-going options! Do you defeat the brain in Cydonia and go on to fight the interdimensional menace, or do you destroy the dimensional alien city and go for Cydonia later?
This will never happen in the TFTD portion of the mod because otherwise that risks dependency on a cross-game, and would also make things super confusing.
4th Idea: There are always the possibility of mutants!With so much alien activity going on in earth, there are bound to be human-alien crossbreeds. You are going to have to manage relations not only with the countries but also the band of mutant clans that form. Will you treat them kindly with their revolution against a rogue agency (aka MiB and so on) and have them help you fight the aliens, or will you just downright obliterate them because of the risk of increased alien infiltration?
Yes, I agree there is a frack-ton of coding involved, but I bet if you share this project with some of the active coders, they could accept to do a bit of the more serious coding work! Maybe have Yankes of the OpenXcom Extended project help you? It might just be worthwhile if you two work together. There are also other good coders out there. Think about it.
Heck, maybe even SupSuper, Warboy and some other source coders could do a bit of work to allow some of this for regular OpenXcom!