Anyway, my thought was that there would be two different ways things could play out. One if you wanted to do the sewer stuff from jail, and the other if you don't.
The trigger would be being in Imperial City with a certain minimum renown. Oh lets say 30, for sake of argument. Enough that you've established a reputation, for good or ill. Once you've met the requirement, you are approached by a member of the Blades, who takes you to meet with Captain Renault (at whatever location. One of the guard towers maybe?). Anyway, she's offering a job. The Blades have heard rumors that something may be happening, and they want backup that no one would know about, and due to your reputation, she thinks you would be perfect.
This is the decision point. You have to either accept or decline. If you accept, you are taken to the Jail, only you aren't "really" a prisoner. (Ideally your equipment would be secreted away somewhere, maybe a short distance into the tunnel? Whatever.) Anyway, things would play out basically as in the Vanilla tutorial, only you don't have to do the divergence through the tutorial dungeon itself. Also since the player will be much more powerful, it would make sense to make the Mythic Dawn assassins more of a challenge. Also provide some sort of extra reward (Renault's armor?) for going through this.
On the other hand, if you decline, you are sent on your way. A few days or a week later, the Emperor will be assassinated. Another adventurer was hired by the blades, but he/she was not as good as you are, and falls on their way to Weynon Priory. (I like your idea of having them be an actual NPC, that would be really cool)