My theory is that the Outsider is simply a part of Corvo's (and other assassins) conciousness as part of a plot to destabilize the Empire (which Corvo had a shot at and may succeed base on your choices).
Corvo's mysterious background makes me think that he might be a brainwashed magic sleeper cell of an outside faction (The Outsider... get it?) that was sent in to bring an end to the Empire; much like many other assassins who ultimately failed because they got soft, foolish, or lose their minds. (like that bird lady).
The sleeper cells' mind have some kind of grand plan programmed in their heads a long time ago that dictates their every action, and magic powers that stay hidden until the right time. The runes are James Bond-like gadgets, left behind by other assassins of the past.
And the fact that at one point, Corvo received off-camera "special forces" training, he might be a powerful piece in the chess board when comparing to the other assassins.
Also, there are more clues pointing to that the Outsider is just a part of Daud's own conciousness. The Outsider said to Daud after he killed the Empress... right when Daud starts to feel guitly about killing her: "I'm here because you're right, the Empress is different".
Since when did an omnipotent god-devil slip off an "Oops, my bad. I should have listened to you in the first place, shouldn't I?" The Outsider realizes failure because Daud's conciousness realizes failure.
The act of realizing failure spring Daud into further action that involves the Brigmore Witches, who might be the outside faction's main obstacle because the Witches practice black magic. It's all part of the plan, see? Daud kills Empress, that mysterious trip that Corvo took, and returning home "In the right place at the right time" as Campbell puts it... Daud was "planned" to feel guity and go to destroy the Brigmore Witches... Then six months of rampant corruption and a mysterious plague, as Corvo is planned to deal the killing blow to the Empire.
But this outside faction's plan can go wrong if any humanity left in Corvo and Daud that refrain them from performing acts that get them high chaos. You know, because of peace and love and sleeper hold! And the outside faction probably didn't plan on Corvo having a daughter (Oh come on, it's out: Emily IS Corvo's daughter) and saving her and putting her on the throne.
Of course, alternatively, Daud's humanity and admiration for the Empress causes him to feel guilty in the first place, which may or may not disrupt the outside faction's plan; and the Brigmore Witches maybe a random faction that is caught in the web. The Outsider simply feels guity because he's Daud's conciousness. A "bug in the program", maybe... Either way, Daud's fate is sealed; with the killing of the Empress, he is no longer useful to the faction. Now he can go die of the plague for all they care.
In a way, you failed your mission if you pick the "Good Ending" with low chaos and letting Emily live; and you let an inevitably corrupted Empire lives on. So in this perspective, the true ending is High Chaos, Emily dies, and Corvo left the country on a boat. (Maybe his job is finished and he is programmed to go back to the faction)
Just a theory of mine, what do you guys think? A lot of room for a sequel.
PS: The faction might be a underwater race of talking singing whales with magic and mindcontrol, plotting to rise up to the surface to take revenge for whaling and to conquer the surface world... It could be legit, since whales live for a long time; they don't mind waiting for the right person to be born and empires to slowly crumble. They're out there... deep in the sea... waiting and watching.
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