It started in world kind of like ours, but also very different.
In that world, the Tunguska event was caused by a meteor, which carried some very funky matter.
How funky? They couldn't even find meteor at first because it's matter was scattered upon impact, and it all replicated the properties of what other stuff it touched, blending in with the scenery.
Once they identified the the funky matter, they researched the hell out of it.
One of the results of that research was of some Tesseract-looking cubes that could generate clean energy seemingly without limit, which were quickly incorporated into other technologies all over the world.
Further research into the funky stuff also led to the creation of the first botegirl. Code G, A.K.A Enterprise, with many to follow.
It was at some point here too that what would become the Sirens were created. As a more conventional form of weapon based on the technologies available. Cause there was a war brewing in the background.
It took them a bit too long to realize that the seemingly unlimited energy that the cubes could generate was coming from somewhere. From higher dimensional space, of which they knew very little. And that's when things started going wrong.
Research into how botegirls work went south when one Bon Homme Richard underwent a horrifying transformation. Becoming something that know nothing but destruction and the corruption of others into doing the same.
Maybe related to the above. Humanity came into contact with something in those higher dimensions the cubes tapped into. Maybe multiple somethings. Entities of concepts, more than matter. Of truly alien nature.
And then they came into conflict. Because of course they did.
Humanity was annihilated. The KANSEN tried to fight the invaders but were almost all wiped out too.
The Sirens, cold calculating machines that they are, came to the conclusion that there was no winning that fight. They decided to let their home burn while they traveled to alternate universes, looking for something that could defeat those enemies. Using alternate Earth's as testing grounds.
An unknown amount of tries later, their modus operandi become to give humanity some select goodies for them to create KANSEN. Then the Sirens make themselves into a global threat to push humanity and the botegirls to their absolute limits and study the results. They also manipulate things in the background, conspiring with locals to orchestrate conflicts that mirror those of World War I and II.
That is all in an attempt at forcing an "awakening" in the KANSEN. A state where they would gain incredible power due to their own extradimensional nature, while retaining their self control.
In many of the "failures", where humanity went the way of the Dodo once again, there were survivors. KANSEN that threw away everything to become better weapons and it was still not enough. Those poor souls undergo a process called simply METAmorphosis, which grants them great power but also leaves them as broken husks. Many of those, including Code G, came together to seek revenge on the Sirens.
The game starts in one of those "testing grounds". Iron Blood (not Germany) and the Sakura Empire (not Japan) broke away from the alliance that pushed back the first major Siren incursion, due to disagreements on how the world wide threat is being addressed, throwing the world into conflict.
In truth, the KANSEN, who do know how WWII is supposed to play out to some extent, were doing everything in their power to break out from the control of the Sirens to prevent that fate. With the Iron Blood in particular going behind everyone's backs and collaborating even with their supposed enemies to strike back and hurt the Sirens in a true and lasting manner.
Meanwhile, some rando from the Eagle Union (not America) navy, with more ties to this crazy plot than anyone could have imagined, gets posted on a base and given command of a few KANSEN. They now have to deal with all that stuff described above.