When Ao cast out the gods from heaven, their avatars walked the earth, interacted with mortals (some more ruthlessly than others) and scrambled to find a way to return to their homes. Known as the Time of Troubles, the Godswar, or the Avatar Crisis, this period in the history of Faerûn is the most chaotic in recent memory.
Sudden mortality wreaked havoc on the deities. Mystra was destroyed and her essence merged with the land, causing magic to function erratically and creating many areas of wild and dead magic. Gond the Wonderbringer fell to earth as a gnome on the shores of Lantan. Grateful for the sanctuary offered by the city, he taught its citizens the secrets of smoke-powder. Tymora appeared at her temple in Arabel and it is thought that per presence there spared the city from destruction. Ibrandul, god of caverns, was slain by Shar and his portfolio stolen.
Helm retained his divine power and was commanded by Ao to guard the path back to the outer planes. Due to his success in the endeavor, blame for much of the Godswar's destruction is laid at his feet. Malar battled Nobanion and was hunted by Gwaeron Windstorm. Shaundakul battled and destroyed the avatar of a minor orc deity, Sharess to the form of the favorite concubine of the pasha of Calimport and was liberated from the growing influence of Shar by Sune. The Red Knight appeared in Tethyr, helping that nation defeat monsters raiding from the Wealdath.
Hoar slew Ramman, Untheric god of war, but lost his foe's portfolio to Anhur. Clangeddin Silverbeard battled Labelas Enoreth over a misunderstanding. Waukeen vanished and custody or her portfolio was claimed by her ally Lliira. The avatar of the godling Lyachtu Xvim, half-demon offspring of Bane, was imprisoned under Zhentil Keep. Gildeam, the god-king of Unther, was slain by his rival Tiamat, ending his two-millennia rule of that nation.
Bhaal, the god of murder, was greatly weakened at the time of the Godswar and existed only as a murderous force that could posses living beings. When Bane challenged Torm, the Black Lord slew all assassins in Faerûn and absorbed their essence, further weakening Bhaal.
Forging an alliance with Myrkul, Bhaal kidnapped the mortal Midnight and discovered one of the tablets of fate. But at the Boaraskyr Bridge Bhaal was killed by the mortal Cyric with the sword Godsbane (the avatar of Mask). Cyric absorbed some of Bhaal's power, while the rest went into the Winding Water, poisoning it.
Leira, goddess of deception and illusions, was slain by Cyric with Godsbane and her portfolio absorbed by him. Cyric later broke Godsbane, greatly weakening Mask.
Bane was destroyed by Torm during a battle in Tantras, and his portfolio was given to Cyric for Ao. Torm himself was destroyed in the conflict with Bane, but because at the time his realm was actually Toril and because he died in service to his ethos (obedience and duty), lord Ao restored him to life and reinstated him as a deity.
Myrkul's avatar battled Midnight, and she destroyed him, Midnight became the new incarnation of Mystra, absorbing the essence of the previous goddess from the land. Cyric became the new god of strife, tyranny, murder, and death, holding the portfolios of the slain Bane, Bhaal, and Myrkul (years later he lost the portfolio of death to the mortal Kelemvor when he was temporarily driven made by an artifact he created.
The close of the Avatar Crisis brought a change to the way deities relate to their followers. By Ao's decree, a deity's power is related to the number and fervor of his worshippers, and do deities could no longer afford to ignore the faithful. While the Godswar reshaped the land and altered the Faerûnian pantheon dramatically, the accountability of divinity is the most powerful legacy of the Time of Troubles.