Several deities were destroyed while some mortals rose to divinity.

Bane was destroyed in a battle with Torm. Bhaal was slain by mortal Cyric using the sword, Godsbane. Mystra was killed by Helm.

Time of Troubles - Synopsis

(Time of Troubles, aka: Avatar Crisis; and, Godswar.)

Trouble was afoot during the Year of the Shadow, 1358 DR, when the gods Bane and Myrkul plotted and subsequently stole the Tablets of Fate from the Overgod Ao. Their reasoning was that Ao would surely reward whoever found and returned the sacred artifact that defined the balance of good, bad, chaos, and law; the same artifact that also defined each of Ao's gods with their particular domains and portfolios. Contrary to what they expected, Ao reacted very swiftly, and very severely.

It is not clear if Ao recognized the true culprits of the crime, or not. He reacted strongly to the theft of the deities' most sacred artifact by accusing all the Gods of being overly self-indulgent and showing little regard for the mortals who empowered them in the first place. Seeking to rout the thieves (as well as perhaps humble some of the more arrogant and selfish gods), he unilaterally stripped all within his dominion of their powers and domains, then cast them upon the face of Toril in their mortal, avatar form. That is, all but one.

The Guardian Helm was the singular exception during this time, and was charged by Ao with guarding the entrance to the Celestial Staircase, the portal connecting the material world to the Outer Planes, home to the exiled deities. A good reason for this, as Ao expected many of the gods to not take well to the material world of Toril and try to sneak home. And, thus, several did try.

A time of unbelievable chaos ensued. Clerics had no spells, unless they just happen to be within a small radius of their chosen God's physical presence. With Mystra stripped of her powers, The Weave became unpredictable and uncontrollable. Gods wandered here and there, and mortals were, more or less, left to fend for themselves. It is said that many mortals did not notice the difference of the 'before' and the 'after', thus confirming Ao's assertion.

During this time, many changes occurred within the Pantheon itself. Battles were fought, gods died, and heroes were made.

Elminster managed to slay the god Bane, who was then revived by his partner-in-crime, Myrkul, only to be slain yet again by the demigod Torm. Torm was also killed in this battle by Bane just before he died.

The mortal Cyric fought against Bhaal, the god of murder, and killed him; however, Bhaal had already foreseen his own demise, and had populated Toril with Bhaalspawn prior to his death, in the hopes his children would someday resurrect him from the plane of Limbo.

Mystra, goddess of magic, was destroyed by Helm when she attempted to bypass him at the Celestial Staircase, hoping to make it back to the Outer Planes, her home where her powers would be restored and she could again gain control of the erratic Weave.

Myrkul, god of the dead, was killed by Midnight, a mortal female wizard wielding the powers of the slain Mystra, on the slopes of Mt. Waterdeep.

Waukeen was missing for several years, and presumed dead. However it came to light after her rescue from the demon prince Graz’zt’s Argent Palace that she had been double-crossed by the evil prince in an attempt to negotiate safe passage across the Astral Plane to the outer plane of Brightwater, her home. Graz’zt had held her prisoner for more than ten years, until she was finally rescued by a small group of mortal adventurers.

There were several lesser gods who also died during this time and immediately after. The ‘immediately after’ usually at the hands of a greater deity wishing to expand their portfolio while the opportunity presented itself.

The shifting of power, the ascension of new gods, and the falling away of old ones all marked a new dynamic in the Pantheon.

Contradicting his own edict that no slain god would be resurrected, Ao did resurrect Torm. A demi-god before he was killed by Bane, Ao restored him to lesser godhood and he became incorporated into the ‘Triad.’

Two mortals were elevated to the state of Godhood by Ao, and ten years later, a principal in the saga of the return of the Tablets of Fate also attained godhood.

The first mortal, Midnight, assumed the position of the slain Mystra, granted her by Ao. Her name also changed to Mystra. (It was reportedly the mortals Midnight and Kelemvor Lyonsbane who recovered the Tablets of Fate.)

The second mortal was Cyric, who had killed Bhaal, with the help of Mask disguised as the sentient sword Godsbane. (Mask had originally thought he would help Cyric and then find a way to strip Cyric of the lies and deception portion of his newly-acquired portfolio.) Cyric originally held all of Bane's vast portfolio for a short time. However, a portion of it was eventually granted to Bane's half-demon son, Iyachtu Xvim.

While still a mortal, himself, Cyric had pursued Kelemvor and Midnight in the hopes of reclaiming the Tablets of Fate from them for his own use, and had ambushed and killed Kelemvor using the Godsbane sword. For ten years, Cyric searched in vain for Kelemvor's soul, hoping to find it and use it as leverage against Kelemvor's once-mortal lover, Midnight, now Mystra, who was Cyric's bitter enemy.

Cyric's obsession with finding him led the mad deity to forming and sending inquisitions to his own Toril-bound churches, paranoid that his congregations were rife with traitors that would be harboring his enemy's soul. No matter what Cyric did, he found no trace of Kelemvor's soul – not even a clue. He did, however, manage to drive many of the faithful away from his churches and this mutiny by the faithful weakened him precipitously. Enough that he was tricked into believing that Kelemvor still lived, and in a mighty rage, smashed the sword Godsbane. The sword shattered, and from the shards rose Kelemvor. He had been trapped by the god Mask since his death, all the time secreted under Cyric's nose. They clashed, and in the end, Kelemvor defeated Cyric in The City of Death. It is said that by an overwhelming vote of confidence of the dead spirits and other inhabitants of the Gray Wastes, as well as Ao, himself, Kelemvor ascended as the God of Death in 1368 DR. He rules humanely and with dignity over his portfolio, and he and Mystra remain close.

It is widely surmised that Cyric became even more unhinged following his devastating defeat at Kelemvor's hand. His dreams of purloining Mystra's Weave for his own purposes had crumbled into dust. We have yet to see how the resurrection of Bane in 1372 DR, and the subsequent murder (by Bane, no less) of the half-demon son holding the other half of the original domain will affect the insane God. The re-establishment of Bane's church may end up being the final nail in the immortal Cyric's coffin, as droves of his once-faithful followers flee to Bane's growing centers of influence.

Thus was the Time of Troubles, the ramifications still being felt today, both on Toril and in the Halls of Gods in the Outer Planes.