Quenta Silmarillion deals with the history of Arda following the entrance of the Ainur as the Valar (see Valaquenta). After the Valar's entrance, Arda was still lifeless and had no distinct geographical features. The initial shape of Arda, chosen by the Valar, was of a symmetrical continent lit by two lamps: one in the continent's north, and one in the south. However the lamps were destroyed by the vicious Melkor. Arda was again darkened, and the lamps' fall spoiled the perfect symmetry of Arda's surface. Two main continents were created that are of concern to the story: Aman on the far West, and Middle-earth to the East, over the Great Ocean.
Following this, Melkor hid himself from the Valar in an enormous fortress, Utumno. He also surrounded himself with horrible beasts, many of them Maiar in the form of fell animals, known as Balrogs. Balrogs were to remain his most faithful servants and soldiers ever after.
The Valar then made for themselves a home at the utmost West, upon Aman. Then the Valar began to reshape Arda yet again, making it habitable and preparing it for the coming of the Children of Ilùvatar (Elves and Men). However everywhere they went, Melkor followed them spoiling the fruit of their labor and damaging their achievements. Thus, the whole Arda was marred by Melkor's anger, envy and lust of power.
Utumno did not protect Melkor, however. He was taken prisoner and sentenced to three ages (about 9000 years) of imprisonment. Utumno was laid bare; but all its evil was not destroyed. Before Melkor was taken captive, Arda witnessed the awakening of Elves, the first-born Children of Ilùvatar. Elves are described as anthropomorphic beings, who, however are immortal and possess many virtues (beauty, health, ability to communicate with the nature), beyond the share of Men. The Elves were met by the Valar and invited to join them in the West; however Melkor managed to reach some of the Elves even earlier. It is said that from them he bred the hideous race of Orcs whom both he and his follower Sauron used as soldiers.
Some of the Elves refused to go westward. They became known as the Avari. Two houses of the Elves, the Vanyar and the Noldor crossed the Great Ocean with the help of the Valar. A third group, called the Sindar stayed on the eastern shore of the Great Ocean, however among them a part of a house called the Teleri sailed across the ocean later.
At some time between the imprisonment of Melkor and his release, the Valar created the Two Trees, Laurelin and Telperion, which filled Arda with light.
There arose a mighty Elf among the house of Noldor, named Fëanor. Fëanor was skilled in crafts and his greatest achievement has been the making of three wonderful jewels, the Silmarili. The Silmarilli contained the light of the Two Trees of Valinor (as the land of the Valar was known).
By that time Melkor's captivity was over. However he returned to evil quickly. Through a vicious design he managed to destroy the Two Trees and to steal the Silmarili. Then he fled eastward, to the Middle-earth .
The furious Fëanor followed Melkor (whom he re-named Morgoth). This was done against the will of the Valar, and during Fëanor's flight he slew many of the Teleri. For this he and his followers were forbidden to approach Aman ever again. However Fëanor ignored this punishment and managed to cross the Great Ocean eastward. There he joined with the Sindar, who had been on Middle-earth all along. Years after this flight, in order to diminish the darkness, the Valar launched the Sun, so that it would dissolve Melkor's shadows.
Morgoth, who returned to Middle-earth with more power than ever, in the form of the Silmarili, built a new fortified capital, Angband. From there he assailed upon the Sindar. However, with the help of the Noldor who had just crossed the Ocean, the first onslaught of Morgoth's attack was thrown off.
Following this, the Noldor settled with the Sindar in the West of Middle-earth, known as Beleriand. They adopted the Sindarin language instead of their native Quenya. However a period of relative peace and stability was short-lived (at least by the Elves' standards). One of the first victims of this war was Fëanor. As the time passed, Morgoth gathered more and more force.
Three hundred years after the coming of the Noldor to Beleriand, Middle-earth witnessed the awakening of Men, the Secondborn (or the Followers). Most of them allied with the Elves in order to defend Beleriand from Morgoth. However neither the Elvish skill, nor the human force succeeded in defying him. One after another, domains of Elves and Men were destroyed and filled with evil. Around that time, the Moon rose for the first time.
At last, more than five centuries after the flight of the Noldor, Eärendil, the son of an Elf-woman and a Man set sail to the West with the only Silmaril that his ancestors managed to recover. He was allowed to land in Aman, and to plead the Valar for mercy towards the Elves and Men.
The Valar agreed to pardon the Noldor. They set out to fight Morgoth and were victorious. Morgoth was expelled from Arda forever. However during the conflict, the very continent of Beleriand was destroyed and sunk, thus forming a new shoreline for Middle-earth, hundreds of miles to the east. However since Morgoth made most of Beleriand desolate as he conquered it, all of the original inhabitants fled to the East, where they were not affected by the conflict.
The Valar offered Elves their pardon and the right to come to Aman. Many of them did indeed leave Middle-Earth, weary of centuries of warfare against the ever-growing evil. The tribes of Men that helped the Elves were given a whole continent of their own, on which they founded the kingdom of Nùmenor.
Eärendil's Silmaril became a bright star. One Silmaril was sunk in the water of the Great Ocean, and the third was lost in the depths of Earth. Thus no trace remained on Middle-earth of the Two Trees of Valinor; but their influence lives on in the elements: air, water and earth.