"Valar Morghulis" says to kill all characters but The Lion And The Wolf says to choose 3 and then kill off all the rest. Which one takes precedence over the other?

After plots are revealed, but before plots are resolved, the player with the highest initiative on their plot card chooses who becomes the first player for the round (see p.8 in the rule book). Thus, the player with the highest initiative may choose to be the first player, or may decide that their opponent should be first player for the round.

The rules state:

"If both revealed plots have "when revealed" abilities, the first player decides the order in which they resolve."

I hope that helps.