Those are sketchy notes at best, but contributions and ideas are still welcome.
The plot-line will follow X3:TC events. Terrans have been discovered, and additional info about Xenon CPU ships have been recovered. However, even if this total conversion will basically follow the X-Universe history, you'll have a completely different role, and most of the storyline will be based on how the universe evolve.
The universe map will be completely different from what you've known so far, mainly to improve results of the Faction AI and AFF libraries. The plot will have to take that into account someway or another.
The map will based on sector clusters tied by trade lanes. Each main faction will get a cluster and a few minor sectors. At game start, most sectors (whole clusters and trade lanes) will be either unclaimed or pirate owned. As the game develop, the different factions will expand across the map.
The Argons, Borons, Paranids, Splits, Teladis and Terrans each get a cluster and will use the usual ships and weaponry. They will be handled by the Faction AI plugin. Relationship between those faction have heavily deteriorated and are mostly back to the point before X2. Argon and Borons will start are allies, and the will be at war with the Paranids and Splits who have settled an uneasy alliance. Teladi will start neutral to everyone but as they got a very good starting position, other factions will be tempted to break the peace treaty. Terrans will be mostly fighting against Xenon forces and will try to avoid getting into politics.
The Pirate Guild will be handled by my Pirate Guild plugin, altered to be used by AFF. The Guild will actively defend pirate sectors and try to take over border regions while offering dynamic missions and trade opportunities for the player.
This faction will be handled by the Yaki Armada plugin. The Yaki won't be able to take much territory, however due to their nomadic nature it won't be a problem. Yakis are nomadic pirate mercenaries, wealthy factions can hire them to attack other factions. As with PG, the plugin will provide the player with dynamic missions and combat opportunities.
As usual, Xenons are merciless AI ships. They will be handled by the Xenon AI and expand in a different way than standard factions. I'm not sure if a “Xenon Start” will be included or not. I'd say no as it would require to set a ECS dialog system for them especially for this start.
This is the hard part. I don't know how to implement them in a Kha'aky way.. Canons like the “jump everywhere they want disregarding jumpgates” doesn't help script wise. Their hive-mind isn't so different from what will be implemented with the CPU Ships in the Xenon AI plugin. At this point, all I know is that (a) modeler(s) will be needed. Default models are ugly, Kha'aks should be organic imho. Moreover several Kha'ak station types have to be added (shipyard, mine and military hq).
A loose confederation of independent sectors that refuse to bend to the dominant powers. The main gamestart will start in one of those sectors and provide tips to unfold the plot. ISA members will come from all races and so you'll find a wider variety of ships and stations. ISA will start at peace with the Pirate and Yaki factions and get a random batch of unconnected sectors instead of cluster.
The goner race slot is kinda outdated now that the Terrans are in the universe. I'm thinking of adding them as a trader/support neutral race disconnected from the dynamic AI. You'll find goner temples and stations in long trade lanes for refuel purpose. They could provide basic trade and taxi missions to the player. In any case they will need a few additional ships and stations.
The whole plot system can be summarized as a dynamic tree system.
Missions will unfold depending on game state and follow different generic paths. For example: Let's say that one of the mission involve the weakest generic faction trying to destroy a research facility of your own faction for whatever reason. Depend on current faction standings, the actors in this mission will be different. And, of course, the impact on the diplomacy will be different, eventually unlocking (or not) a new mission.
End plot results will also be based on the game stat - which in turn, will be heavily influenced by the result of previous missions. As an example, if the Xenons take over 60% of the map, the plot will be lost and Xenons will receive a bonus. On the other hand if you or your faction annihilate all CPU ships, they will be critically crippled.
Of course the player can completely ignore the plot and live his own life.