Who were the Agarthans? A Summary of Ancient Fodlan History (spoilers)
The lore is found primarily in the Verdant Wind route with some CF, SS, and Shadow Library. Full spoilers for the entire game.
Sothis came to Fodlan possibly from another world (the Blue Sea Star also possible ties to other FE games but that's another post) where she and her Children of the Goddess ruled over humanity guiding their development and civilization.
Not all humans were satisfied being ruled over by immortal non-humans, some wanted self rule and independence, what followed was a war on such a scale that the land was destroyed. There's implications that this was maybe a nuclear war that radically changed the geography of the continent. The human independence movement lost and were driven underground by the apocalypse above ground. The Agarthans thus see themselves as the true humans.
The next part as with many things is unclear but Rhea recounts that Sothis sacrificed herself to restore the land and fell into a regenerative coma or died I'm not sure. The Children of the Goddess continue to rule humanity in Sothis' absence awaiting the day of her revival. The main civilization of the Children of the Goddess lived in was in what came to be known of the Red Canyon, those that lived there were known as the Nabteans.
Fodlan was peaceful for some time but deep underground the Agarthans had been biding their time and began pulling strings around Fodlan from the shadows. Their first puppet was Nemesis and their last is Edelgard. The Agarthans set up Nemesis to raid the Holy Tomb and steal Sothis's body, heart, and blood for them. From Sothis's body the Agarthans craft the Sword of the Creator, from her heart the creststone, from her blood the crest of Flames. These they give to Nemesis so that he may be a more useful tool against their old enemy the Children of the Goddess and their religion worshiping Sothis.
Nemesis' forces slaughter the Nabateans and the canyon runs red with their blood. From these new bodies, hearts, and blood, the Relic weapons and crests of the Ten Elites are made. Nemesis and the Ten Elites then uniting the forces of humanity (who have no idea about any of the above due to information suppression and the passage of time) and begin. Thus the crests of the Ten Elites can be found primarily in Faerghus and to a lesser extend in Leicester.
Rhea one of the few surviving Children of the Goddess (along with the Saints) goes mad with grief and obsesses over reviving Sothis swearing revenge on Nemesis. She takes on the name Seiros, finds a pawn of her own in Wilhelm I. She helps found the Adrestian Empire and the Church of Seiros. Seiros and the Saints give their blood and thus crests to their allies and thus the Saint's crests can be found in the Adrestian nobility.
These two forces clashing was the War of Heroes where Seiros won and killed Nemesis in the Battle of Tailtean. Rhea then immediately set out to rewrite history but Nemesis and the Ten Elites were widely popular among the population so she couldn't just say they were evil without people revolting. Instead she concocted the convoluted propaganda you hear in the game of how their powers were gifts from the Goddess to fight evil gods but they fell to hubris or something. Nemesis's corpse was retrieved by Agarthans and cryogenically preserved and revived and he was turned into a zombie thing (not sure exactly what he ended up as).
Rhea then proceeds to hold Fodlan in stasis for the next 1000 years because she sees her role as preserving Fodlan as it is, waiting for Sothis to return. The Agarthans sink back into the shadows pulling strings from behind the curtain and subtly undermining the stability of Fodlan biding their time to take another shot at the Church all the while doing more human and Children of the Goddess experiments to create more powerful weapons. Their most recent success in all this and most recent shot at the Church is with Edelgard. To be clear a lot of people hate the Agarthans because they ran a lot of cruel human experiments including to one make a person with two crests and tortured Lysithea, Edelgard, and their families to do so.
Funfact: one of my favorite crackpot tinfoil hat theories is that the Agarthans might be the remnants of the irl United Nations and that Fodlan is a post apocalyptic modern real world Earth. The main evidence is that their symbol looks suspiciously similar to that on the UN. The UN has a globe stylized as a map of the continents on a grid surrounded by a laurel wreath. The Agarthans have a similar grid except the continents have been replaced by an eye surrounded by a stylized laurel wreath that resembled electronic circuits. There's more circumstantial evidence like the Agarthan's access to seemingly modern technology like ICBMs or how if you translate the cyrillic in Shambhala (VW and SS) it has a bunch of nuclear warning signs but in magic terms (like deadly light and such I don't exactly remember), there's the cyborgs and what look like computers all hinting at a modern or futuristic civilization. And then there's how the Agarthans claim to be the true humans. In the end there's no definitive proof but I think this is a fun hypothesis to think about.
There's 2 wars or I guess you could consider them a continuation of each other. The first was very ancient and led to large scale (possibly nuclear) destruction, this is the one that led to Sothis' death or regenerative slumber I can't tell if they were talking metaphorically about sleep or not since Children of the Goddess like Flayn and Byleth enter regenerative sleeps after great injury. The Nabateans ruled as benevolent dictators seeking to guide humanity awaiting Sothis' return. Like in the first war not everyone was happy with Nabatean rule. Many humans wished to rule themselves and determine their own destinies (essentially a human ethnonationalist independence movement). The Agarthans backed Nemesis providing him weapons and technology to fuel his war and in exchange he gathered Nabatean bodies for them. The pillars are light are implied to be Agarthan nukes.
