Larian Studios Forums Baldur's Gate III Baldur's Gate III - General Timeline of Events

Ilyn Toth was the Necromancer of Thay. He was trying to resurrect someone important to him who most likely had some sort of information or artifact that he was after. I determined it was likely someone with important information because one of his notes mentions that he questioned the corpse using Speak with Dead, but it didn't tell him what he wanted to know. Why would he question the corpse of his daughter or wife? It most likely was someone who had important information he desperately wanted.

He stole the Necromancy of Thay book from Szass Tam, the Emperor Lich King of Thay, and he fled to Moonhaven with his apprentice Eliette. He also fled with the body of the person he was trying to resurrect. He pretended to be the pharmacist at the apothecary in Moonhaven so that he could conduct his undead experiments in his basement lab. He sent his familiar out to tail the children and potentially even adults of the town, which helped him to abduct them and use them in his experiments. That's why they started vanishing, and no one was the wiser. I believe his familiar would poison them so that they would fall to sleep or be unconscious, and then he'd just show up and take them down to his lab by night, but that's speculation. All that is really mentioned is that his familiar made it easier to abduct his victims.

Eliette is a High Elf apprentice, and she hated him, which is in the journals. It is clear at one point that Eliette is the apprentice, and we know that she is the spider matriarch because she says that her name Eliette has no more meaning for her.
She's almost forgotten it. We also know that the apprentice stole the keygem and that she escaped into the well during the Dark Justiciar attack.

She only stayed with Ilyn Toth because of some vow she made that she couldn't break. She even later expressed that she was so elated that the Dark Justiciars murdered Ilyn Toth so that she was at last free from him. It was Eliette who stole the keygem of the Necromancy of Thay, and Ilyn Toth was suspicious of his apprentice's treachery. He was even sending his familiar to follow her into the well to see what she was up to. The Dark Justiciars, led by Ketheric, however, interrupted everything, and he was killed. Eliette escaped into the Whispering Depths, but it is clear she was later kidnapped by Drow and taken to their fortress. Later, some drow traitor killed the Matriarch of the House that Eliette was a slave to, and she escaped back to the Whispering Depths. Being an elf who lives forever, she lived for over a hundred and twenty years, for the events of Moonhaven's destruction were in 1372. Who knows how long she was in drow captivity, but she escaped and had become quite insane. She believed that Lolth herself was visiting her in dreams and prompting her to delve into arachnomancy. Finally, she was visited by a drow arachnomancer who was killed. She took his stuff and his tomes and knowledge and learned how to change herself into the Phase Spider Matriarch.

And so, she is the Phase Spider Matriarch High Elf Apprentice to the Necromancer of Thay. She has transcended her original form to take on the form of something so much more terrible.