Mystra's history is a complex thing, both in and out of setting. She's died multiple times in universe for reasons that were both narrative, and as a result of real-world editorial fiat. The last time Mystra died was as Dungeons and Dragons was shifting from 3.5 into 4th edition. At time time, the design team was pushing to trying to drastically simplify the lore of the Realms, and arranged for this state of affairs by having Mystra killed by Cyric. This unleashed the Spellplague, an enormous magical disaster that took out the Weave, changing the function of magic all across Toril. At the same time, a part of the world that had been separated in the earliest history of the Realms, Abeir, began to reassert itself, rejoining itself to the world in certain places, both the Spellplague and Abeir physically altering the face of the planet. Many gods were revealed to actually be different deities, and yet others were slain as Mystra had been. The setting itself took a large leap into a future point in time. A lot of extremely popular mortal characters passed away during this timeskip.
The result of all of this was a Realms that had been drastically changed from what it had been before, and the fandom absolutely rebelled. A large number of people who had been fans of the Realms for decades decided they wanted nothing to do with what Wizards of the Coast had done to the world. In the name of slaughtering the sacred cows, they essentially murdered a silver goose.
Meanwhile, in D&D proper, 4th edition's ruleset had proved unpopular with many people. They opted in 5th edition to create something more similar to what had gone before.
They ultimately ended the Spellplague by reversing a large number of the changes that had been made to the setting in the "Second Sundering" event. Mystra was returned to life, dead gods like Eilistraee and Azuth were revealed to be not so dead, parts of the world were returned to previous form when the Spellplague ended. This is the context in which the 5th edition was released, and the state of the world in which BG3 is set, in the aftermath of two calamities.
