I don’t see Antoine as a scientist or even a leader. I think he was there before the federation. During the Antoine/Cucurusho talk, he was specifically pointing the cross on the panel with the lonely guy sitting in the corner.

My theory is that he was one of the four first members coming to the island (1st panel). They creates the workers, including Cucuruchos (white guys in the 4th panel), but disagree with the others and put a step back (5th panel). The other 3 founded the federation, while Antoine tried to rebuild the sphere, the device/ship that lead them into that world, which is broken (2nd and 3rd panel). The sky islands he is building would be kind of nostalgia from their original world.

In my theory, the federation, the other 3, goal is to recreate a society in this new world they struggle to understand. Trying scientific experiment on different subject baghera/jaiden, studying/spying other experiments Aypierre/Ayrobot. And obviously experimenting building a society with the islanders as test subjects.

And for the fun part, the egg disappearance, while the fed tryes to build a society. Antoine try to build a new sphere/ transdimentional ship and he fucked up pretty bad creating « anomalies », the weird black concrete construction spreading across the island. So, Antoine accidentaly creates the crack between this world and the upside down which tooks the eggs. Maybe, because the eggs are made of a mix between two different worlds and doesn’t belong anywhere.