Leira was ambushed by her supposed ally (Mask) and Cyric, shortly after Cyric ascended to godhood.
Waukeen attempted to circumvent the rules about gods getting back to their domains by loaning her divinity to Lliira, and then arranging for a demon lord (Grazz't?) to transport her to her home realm. Of course, you should never trust a demon lord to keep his promise, and the demon lord betrayed her and kept her hostage while he picked her brain for information. (For Duty and Deity adventure)
Bane was killed twice, if I recall correctly. I do remember once was by Torm. Pretty much, Bane had sucked in the power of all the assassins of the world (weakening Bhaal). So, in order for Torm to oppose him, he got his followers in Tantras (who were attempting to turn Tantras into a stronghold of Torm, by persecuting/executing followers of other gods, even GOOD gods) to redeem themselves by giving their life energy to him. Torm and Bane died in the fight. Torm was reborn after the Time of Troubles, because Ao said he died in the performance of his portfolio ("duty" being the portfolio, if I recall correctly).
Bhaal, as I stated, was sucked dry by Bane. Cyric murdered him by some river, leaving the river poisoned.
Mystra got some information, and wanted to ascend to the heavens to talk to Ao. Helm, in performance of his duty (guarding the entrances to the heavens), killed her. However, Mystra had set up a contingency plan, and had prepared Midnight to assume her place. In the meantime, Elminster had to hold what power he could. But he couldn't cast anything, because he couldn't control that much power. So he had to rely on the Rangers Three for protection. (Shadows of the Avatar trilogy)
Myrkul invaded Waterdeep at the head of an army of undead. Somehow, Mystra/Midnight killed him.
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So, of the deities which died and disappeared during the Time of Troubles (and immediately afterward):
Bane was killed twice. He was finally put down by Torm. His contingency plan, Xvim Iyetchu (spelling?), worked out perfectly. (Or did Xvim just pretend to split apart to be reformed into Bane?)
Bhaal was deprived of his worshippers by Bane, and subsequently murdered by Cyric, using the sword Godsbane (the avatar form of Mask). The remaining essense of Bhaal lives on in some river. (Barring the Throne of Bhaal computer game, of course.)
Myrkul was killed by Midnight/Mystra. He still lives on in an artifact, and is not inclined to attempt godhood again. He enjoys not having to deal with the restrictions.
Leira was murdered after the Time of Troubles. (Or maybe she just convinced the god Cyric that he defeated her, in an attempt to protect herself from a rather powerful and predatory adversary. After all, her only ally, Mask, was the one who set her up....)
Waukeen was held hostage by a demon lord, but an adventuring party set her free.
Mystra died at the hands of Helm (and Midnight/Mystra was later imprisoned by Helm...).
Torm died fighting Bane, but was subsequently reformed by Ao.
And this isn't even taking into account the lesser gods, or the gods from the other pantheons. There was a god of darkness underground (Imbrumal, or something like that...), murdered by Shar, for instance.