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In Faiths and Pantheons, I found:

Mystra is the third deity to hold the position of Lady of Mysteries and Mother of All Magic since the rise of Netheril. The first was Mystryl, who died saving the Weave from the arrogance of the Netherese archwizard Karsus. The second Lady of Mysteries was the first to create the Chosen of Mystra, including Elminster, Khelben, and the Seven Sisters. She died at the hands of Helm during the Time of Troubles while trying to return to the planes. At the end of the Avatar Crisis, a mortal wizard named Midnight assumed the name of her predecessor upon ascension to divinity. ...

And in Magic of Faerun, I found:

Her (Mystryl's) death caused magic to cease functioning across the universe, instantly slaying the upstart Karsus. The deity was reborn as Mystra, and she was able to repair the Weave so that such powerful magic was no longer possible. The new deity shared the same close ties with the Weave as her predecessor. This was proven in the Year of Shadows (1358 DR) when she was slain in Waterdeep in battle with Myrkul and other powerful beings. When her essence merged with the land, magic ran wild in some areas and stopped completely in others. ...

So, was Mystra killed by Helm, or by Myrkul and other deities?

In the books The Avatar Series, Mystra was taken as a prisoner and she binded her essence to a pendant. There was a young girl that traveled with Adon and Midnight and Cyric. The young girl which had the pendant wore it. The group traveled to Waterdeep where the young girl possessed with the power of Mystra's essence battled Helm upon the stairway to the God's Realms. Now it was to my knowledge that Bane and Myrkul took Mystra's true avatar form, or her other half prisoner and in result killed her, leaving her pendant essence left.

Prior to the Time of Troubles and Ao banishing all the Gods to Toril several deities had taken steps to retain some of their power by secreting it away in the mortal realms. Mystra had scattered a number of objects amongst her faithful as insurance against such an event

One particular item, a pendant of some power, was placed in the hands of a young woman called Midnight. After Ao banished the Gods Mystra in a mortal avatar was captured by Bane before being able to regather her power.

She was held prisoner for some time in Bane's Castle Kilgrave in Northern Cormyr, but retained sufficient ability to direct Midnight to try to rescue her.

This is all detailed in "Shadowdale", the first in the Avatar series and there is a thread on wotc discussing just the question you raised

http://boards1.wizards.com/archive/inde ... 54892.html

Mystra eventually escaped Bane, I won't spoil things by revealing how. After reclaiming the pendant from Midnight she set about her attempt to return to the pantheon. Here it was that she encountered Helm, the only deity left his power by Ao, and died trying to win passed him on the celestial stairway.

As I recall, Mystra actually survived (sort of) the battle with Helm.

She was reduced to what was described as basically a magic elemental, and was totally destroyed/dispersed through the Weave when she destroyed Bane's Avatar in Shadowdale.

Though, probably only the new Mystra and Adon know about that, as far as pretty much everyone else, mortal and divine knows, she was killed by Helm.

That bit from Magic of Faerun is really odd. Whichever way you look at it Mystra was dead by the time of events in Waterdeep. Midnight in point of fact killed Myrkul with the fragment of Mystra's power she was carrying.

Um, pretty up on my Tormish lore, Bane was slain in Tantras by Torm.

Actually, Bane went down in BOTH places. His avatar went down in Shadowdale, but Myrkul was around to pick up the pieces then. After the Bane/Torm incident, Myrkul didn't bother, having his own plans for the tablets.

Yes, Myrkul knew about how to raise a god, he gathered all the shards of Bane from the etheral plane, and pieced him back together. It was actually very intresting and cool.