Returning the letter to Mynisera completes one part of the Emperor's mission. Your prizes for getting to this point? If your reputation is high enough, you'll receive some letters (anonymously) telling you about the Numidium. The number of letters depends on your reputation with the various factions (there are seven of them). The more factions that like you, the more letters you'll get. They all say the same thing. But it's a good indication of who really likes you. You'll also receive a threatening letter telling you to lay off Lysandus. And as an added bonus, you get frequent visits from assassins who carry notes telling you to lay off or that you need to be taken care of at any cost. The latter letters are signed "--W". Now who do you know with the initial "W" who might want you out of the way? Three guesses and it ain't Willie Wonka.
Now that you've disposed of one mission, you need to pursue the other -- putting Lysandus' ghost to rest.