The morse code - FFE lore says that the Thargoids tried to communicate with Humans several times before the first war, they even invented translators, but (for whatever reason) humans ignored them. The Thargoids were apparently quite upset that we wanted to fight them! The probes using morse code may well have been the Thargoids trying to communicate with us.
I am pretty sure humans shot first in the war back then, and I am pretty sure they shot first this time as well. Also looking at INRA and their focus on warfare and genocide. AEGIS is heading in the same direction now.
Merope is clearly a center of something Thargoid related. The crashed Thargoid ships that have been found are dated back about 100 years, so there's something going on for a while now and I am pretty sure the superpowers new all along, and according to all the conspiracy stuff they used the cold war as an excuse to gear up on weaponry. Perhaps Merope is some kind of beacon and that's why the Thargoids swarm it?