The Time of Troubles

In 1358 DR, the gods were cast out of their otherworldly domain and made to wander the land incarnated as mortals. In seeking to recover their divinity, they warred among themselves. Magic became unpredictable, and the prayers of the faithful went unanswered. Some of the gods-turned-mortal were slain, while a handful of mortals ascended to godhood, assuming the responsibilities of the dead deities. (Sword Coast Adventurer's Guide, 2015)

Faiths and Avatars, 1994

The Time of Troubles was an exception to many of the normal rules for how deities work in the Realms. During the Time of Troubles, the powers of the Realms were forced to either place all of their divine power in one mortal avatar or, if they exist on multiple planes, were forced to create avatars upon whose existence their entire future divine connections to the Realms were staked. Since the powers of the Realms were forced to stake so much on their avatars, these avatars were acutely vulnerable. While the death of an avatar did not mean the death of the power (Bane and Bhaal, at least, went through multiple avatars in succession before finally dying), powers could only maintain themselves in one avatar form and could not connect with their homes and power bases in the Outer Planes (if they had them).
However, during the Time of Troubles, the general rule that only a deity can kill anything other than a demipower was not violated. Bhaal was killed by Cyric using the sword Godsbane at Boareskyr Bridge. Godsbane was Mask in sword form (evidently an avatar form of Mask). Thus, a power killed a power. Midnight used a disintegrate spell to kill Myrkul in Waterdeep and then used a dimension door to move the dead avatar’s body over the Sea of Swords. At the time Midnight held within her some of Mystra’s divine essence, transferred to her through a pendant in the form of Mystra’s symbol that merged with Midnight’s flesh during her travels. So, once again, although through a slightly circuitous path, a power killed a power.
Mystra died at Helm’s hand on the Celestial Staircase, trying to gain access to her home plane. Before she battled Helm, she had transferred a great deal of her power into her Chosen, Azuth, the Magister, and Elminster. As she died, she gave Midnight the pendant with some of her essence and spread the remainder of her power into the magical weave that surrounds and permeates Realmspace. Elminster was able to call back a ghost of her presence as a sort of magic elemental to kill one avatar of Bane’s, but it was not strong enough to permanently destroy him, and his essence was able to be gathered together by Myrkul and then transferred to a new avatar. Ultimately, Torm killed Bane in Tantras. Again, in the cases of Mystra and Bane, one power killed another.
Gods who were dead at the end of the Godswar were dead in the Realms unless at the end of the Time of Troubles Ao reinstated them himself, as he did for Torm. However, only deities whose only worship ties throughout the many crystal spheres were to Realmspace could have completely died. Any deity who had ties to other crystal spheres would not have ceased to exist. Ao has influence over the powers of the Realms, not the panspheric and multidimensional universe. Rather, all divine ties between that power and the Realms would have been severed. The power itself would not have been dead, but might as well have been for any inhabitant of Realmspace.

Forgotten Realms Campaign Setting, 2001

Seeking power over other deities, Bane (in his previous incarnation) and Myrkul (the former god of the dead) stole from Lord Ao the Tablets of Fate, divine records that state the responsibilities of all the deities of Faerûn. This act convinced Ao that the gods were unconcerned with their worshipers and more concerned with their battles against each other. To punish them and force them to attend their followers, Ao forced the deities out of their extraplanar realms and into mortal bodies called avatars.

The Avatars

The divine avatars walked the earth, interacted with mortals (some more ruthlessly than others), and scrambled to find a way to return to their extraplanar homes, for the normal paths were barred. Known variously as the Time of Troubles, the Godswar, and the Avatar Crisis, this period in the history of Faerûn is the most chaotic in recent memory.
Sudden mortality wreaked havoc on the deities. Helm alone retained his divine power and was commanded by Ao to guard the path to the Outer Planes. Because Helm was successful, much of the destruction caused by the Avatar Crisis is laid at his feet. Mystra was destroyed and her essence merged with the land, causing magic to function erratically and creating many wild magic and dead magic areas.
Gond the Wonderbringer fell to earth as a gnome on the shores of Lantan. In gratitude for the sanctuary, he taught the Lantanese the secrets of smoke powder. Tymora appeared at her temple in Arabel, and it is thought that her presence there spared the city much destruction. Ibrandul, god of caverns, was slain by Shar in secret and his portfolio stolen.
Malar battled Nobanion and was hunted by Gwaeron Windstrom. Shaundakul battled and destroyed the avatar of a minor orc deity. Sharess took 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 on the isle of Ruathym over a misunderstanding. Shar and Selûne fought another round of their age-old battle as mortals in Waterdeep. Waukeen vanished, and her ally Lliira claimed custody of her portfolio for safekeeping. The avatar of the godling Iyachtu Xvim, half-demon offspring of Bane, was imprisoned under Zhentil Keep. Gilgeam, 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 during the Godswar and existed only as a murderous force that could possess living beings. When Bane challenged Torm, the Black Lord slew all of the Bhaal-worshiping assassins in Faerûn and absorbed their essence, further weakening Bhaal.

The Mortals

Forging an alliance with Myrkul, Bhaal kidnapped the mortal wizard Midnight and discovered one of the Tablets of Fate. But at the Boareskyr Bridge the mortal Cyric killed Bhaal with the sword Godsbane (the avatar of Mask). Cyric absorbed some of Bhaal's power, while the rest went into the Winding Water, poisoning the river.
Cyric then slew Leira, goddess of deception and illusions, with Godsbane and absorbed her portfolio. He later broke Godsbane, greatly weakening Mask.
Torm destroyed Bane during a battle in Tantras, and Ao later gave the Black Lord's portfolio to Cyric. Torm himself was slain in the conflict with Bane, but since his realm at the time 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, who destroyed him. Midnight became the new incarnation of Mystra, absorbing the essence of the previous goddess from the land. Cyric became the new deity of strife, tyranny, murder, and death, holding the portfolios of the slain Bane, Bhaal, and Myrkul. (Years later, Cyric lost the portfolio of death to the mortal Kelemvor when he was temporarily driven mad by an artifact he created.)
The close of the Avatar Crisis brought a change to the way the deities of Faerûn relate to their followers. By Ao's decree, a deity's power is in part derived from the number and fervor of his worshipers, and so deities can no longer afford to ignore their faithful. While the Time of Troubles reshaped the land and altered the Faerûnian pantheon dramatically, the new accountability of divinity remains its most powerful legacy.