I want to share with you that the beta branch is being updated with a new story/conquest mode that will replace the Siege mode. I realized that I cannot do what I want to achieve with the Siege, having a gigantic map with all the missions when also the character can fly everywhere.
So I decided to take another approach, In the story mode there will be some in game cinematics that will drive the story.
The "lobby" will be the planetary view where you can go to different locations that will be unlocked, each of them is a level, where there will be 2 or 3 missions. In general one of them will always be to capture or destroy the location/town. If the location is captures the population there will be force to provide resources for you, then you can use the resources to buy support troops or different items. There is a negative side of capturing a location is that the population can rebel and can launch a counter attack and then you need to act against them again, if you choose to destroy it, they will be silent forever. Some locations will require the mothership to be destroyed.
The levels will be increasing in difficulty being the last one Brimir. Also the human forces will be able to launch attacks to the mothership using nukes, spaceships or superheroes.
So keep an eye on the beta branch for new updates.