Much of this has been boiled down and summarized to spare you the agony of long, winded explanations.
The first era (an era is 1000 years) of mortals was harmonious and productive. Civilizations were built and flourished. Cultures interacted, traded and learned from one another, coexisting peacefully through a time when this world was an idyllic paradise. Near the end of this era, infighting between Odinspawn nations began to erupt, resulting in a three-hundred year period of bloodshed and conflict that had been hardwired into their physical makeup by Odin himself. When the dust had settled and the bones had sank into the earth, only one mighty empire of Odinkin remained. But the centuries of expansion and bloodshed had left them with a taste for power and war.
They set their sights on Whiteguard.
The White War
The White War was a long and brutal one. Whiteguard had superior warriors, leadership, equipment and tactics. Odinkin had the sheer force of numbers. Legions of warriors who believed that the worth of an individual could be decided only on the battlefield. War had become the focal point of their culture and spirituality. Despite never making much ground in the grand scheme of the war, Odinspawn would not yield, nor relent in their pursuit of victory. It wasn't long before the Bahamir came to the aid of Whiteguard, creating an alliance to crush the Odinkin foe, putting them back in their place. Feeling left out, Hades decided to directly interfere.
In a shocking twist, Black Mages joined the battle, not as allies of Odinspawn, but enemies of Whiteguard and their Bahamir allies. This resulted in the equivalent of a World War, and mass destruction of the civilizations and relationships they built. Hades had interacted with mortals, commanding his Black Mage tribes to destroy Whiteguard, the Bahamir Dynasty, and then the world of Odinkin. This was the first transgression of the Pantheon, and Bahamut's heart was breaking as he watched his beloved creations fall into chaos.
The war came to a climax with one crucial battle at the Plains of Turra. Each of the races amassed their forces for what would be the largest battle in the history of the White War. Aroused by the prospect of the destruction about to unfold, Hades joins the battle alongside his Black Mages. As the fight begins, Hades is raining down an unholy brand of death upon the battlefield. Feeling the loss of every White Mage, Alexander joins the fight, going head to head with Hades. Feeling as if it were only fair at this point, Odin, Sleipnir and Gilgamesh begin to do what they do best; make violence seem like an art form. It takes hold like a domino effect, and one by one deities join the battle (the Bahamuts, Ramuh, Shoat and Doomtrain not withstanding). When Bahamut has had enough, he steps in. And his wrath is absolute, however just.
The cloudy sky rips open and Bahamut ZERO penetrates the atmosphere, hitting the battlefield with a Tetra Flare, killing the armies of all involved parties. Only the soldiers present. Only the soldiers carrying the torch of that war. Only those actively committing the bloodshed.
Every deity, including the Bahamuts, were sealed in a state it's hard to really explain, but I call it an 'Essence.' They exist, but are frozen in time so that they cannot think, act or use magic until a mortal possessing their Essence 'summons' them. At which point, said mortal individual can command their will. The deity knows what you want it to do, you don't even have to speak. An Essence must exist in either an object crafted by a mortal, or a humanoid mortal being. It is impossible to destroy the essence of a deity.
Bahamut placed the deities in objects in the possession of the Bahamir Dynasty.
The Mana Tree
The bodies of those slain by Bahamut ZERO are buried on mass where they died on the Plains of Turra. A massive, towering tree has grown out of the ground. It's leaves never decay, even in the coldest, harshest of winters. People from all corners of the planet still make the pilgrimage to the tree to be moved by what they call "the atmosphere around it."
The Fall of The Bahamir Dynasty
In the era following the White War, chaos would once again take hold on mortals. Struggling to understand what had happened, and mourning their fallen, there was a brief time of peace for contemplation. When Bahamir diplomats traveled abroad to inform world leaders of the artifacts they now possessed, war over the prospect of obtaining such power was inevitable. Another world war ensued, and the Bahamir Dynasty was picked apart by the rest of the divine races. One by one artifacts fell as regions were defeated and failed to evacuate the artifacts in time.
The Great War
In the centuries to follow, the races one again met of the battlefield, with another world war ensuing. Without Bahamut to step in, the scale of destruction surpasses the White War. During the chaos and bloodshed of the battle, Phoenix strikes Icen down, killing him (this was important because in the written story Shiva was the first deity uncovered by a female antagonist named Lyra Stratta. When she 'summoned' her, she was unfrozen from that moment when she was about to Diamond Dust the entire battlefield to avenge her son. Instead she ended up killing a small element of Zenobian special forces that were accompanying Lyra, thousands of years later. It was how the entire process and purpose of the 'summons' as actually introduced and demonstrated, and a great symbolic moment for Lyra). That climactic battle saw an end to the war when several Time Mages interfered. The summons were gathered by force, placed in artifacts, and hidden away.
The Bahamir retreated into the wilderness. They formed several large tribes, one containing the Imperial family. They remained on the move in dense, unsettled northern and eastern lands. Their sole purpose to protect the Bahamuts.
The Empire of the Odinspawn claimed the larger victory over Whiteguard in the war, and enslaved many of them during the long exchanges of the conflict. Whiteguard worked out borders and were permitted to keep their capitol.
Black Mages denounced Hades, Essences and Magic. They retreated to the savage wilderness of the Veldt, generally considered uninhabitable due to the harsh ecosystems. They remained tribal for all five mortal eras, developing an extremely advanced martial art oriented around mastering the senses enough to defeat armed foes using nothing but mind, body and spirit.
Each Essence was hidden away in a secret location, with only the three Bahamuts remaining on the run.
Over the next two mortal eras, the wars are forgotten. The Essences are forgotten.