The connecting record
statedForgotten Realms Campaign Guide · 2008
Cyric killed Mystra in Forgotten Realms Campaign Guide.
What each of them is ranked on
The killer · Cyric · rank 5
The Prince of Lies — realms
He is the reason the entry two places above him sits where it does. Mystra is third here for what her dying costs the Realms, and Cyric is who killed her the second time: the Weave came apart, the Spellplague followed, and both the setting and the edition were rebuilt around the wreckage. It is the largest consequence any single act on this page has produced, and it was a murder rather than a war.
statedForgotten Realms Campaign Guide · 2008
Mystra's death wrecked the bonds that held the Weave together, and brought about the Spellplague.
statedDragon #378 · 2009
It was the Prince of Lies who murdered Mystra and caused the Spellplague.
The victim · Mystra · rank 3
Magic itself, twice killed — realms
Killing her breaks the world, and the Realms have run that experiment twice. She is the goddess of magic in a setting where magic is a physical system she personally maintains, so her death during the Time of Troubles and again before the Spellplague did not merely remove a deity — it corrupted spellcasting for everyone alive. Ranked on consequence, which is the only entry here where the consequence is a rules change.
statedForgotten Realms Campaign Setting
Maintains the Weave, the structure through which all arcane magic in the Realms functions.
shownForgotten Realms: Avatar Series · 1989
Killed during the Time of Troubles, with catastrophic effects on magic.
What this does not settle
One death in one work. It is the only place the record puts these two in the same room, and it is evidence about that meeting and nothing wider — not a general matchup, not a rematch, and not a ranking of its own.
The ladder above it is argued from everything either of them has been shown doing; this page is argued from one citation.
Where the two disagree, the disagreement is the point, and it stays visible rather than being resolved by whichever of them happens to be on this page.