Well, I have an idea that has been playing in the back of my mind for quite a while, basically... it's post Xenonauts, or in this case post-"Praetorian Invasion". The world has been saved (with hundreds of millions confirmed dead, with tens of millions MIA at best, much of the infrastructure has to be rebuilt, etc.) and all that needs to be done is pick up the pieces.
Problem is, despite the Xenonaut's best efforts, the major powers of the world -be NATO aligned or Pact aligned nations- have gained control of various minor Praetorian bases, allowing them access to Praetorian technology. This has upset the balance of the Cold War, among other things. So, the Xenonauts became essentially GDI and quickly started setting up facilities all across the world (and in the late '90s, in space) to help keep the situation from going out of control. Thanks to a leak from Xenonaut probes, everyone has discovered that there is alienium and the base components of Alien Alloys -aka 'Praetorian Alloys'- in them hills and started a massive race of space colonization.
In addition to this, the Xenonauts discovered that humanity has psionic abilities, just nothing like the Praetorians and their thralls, mostly empathic and minor telekinetic (with the latter being what the Praetorians wanting) abilities. In an unanimous decision of all the departments, the Xenonauts have made an entire section of the organization simply dedicated in getting now-budding psions from pretty much everyone else, knowing what would happen if they don't.
The Xenonauts have bee trying to keep the peace in Sol for decades, but one incident in the Jupiter Sector would lead to war...
Another idea is basically the 'post-Xenonauts' setting above and having the Xenonauts discover -via the largest Praetorian base on Earth- that the Praetorians have discovered an alien energy signature on the moon near Tranquility Base that has them scared shitless, so the Xenonauts -once they got the equipment- sends a team to the area and investigates... discovering a Chozo facility dedicated to observing humanity. The Xenonauts quickly build humanity's first base on the moon -also called Tranquility Base- around the entrance and quickly gave access to the site a Black Omega rating. With complete and utter care, the scientists, archaeologists, and engineers at Tranquility Base uncover the secrets that the facility holds, and learn more about humanity in the process.