The Crocodile's Scales (Main Quest)
Begin this search for the most powerful of the Order's second wave lieutenants in the town of Soknopaiou Nesos, in Faiyum.
Use Senu to pinpoint your informant's villa.
No one's home, but you can investigate inside. Clue include the scattered scrolls and dead dog on the ground floor, an impales child's doll and more scrolls above, but it's the uppermost clue, in the pigeon roost, that advances the plot.
Track the servant to the Beached Trireme camp west of town.
Recon shows him held in the cage toward the far end of the camp, against the rock bluff.
You can fight your way through the whole camp if like, (though if you do the side quest Rebel Strike, you'll sweep through here with a small army later), but you can also just approach over the cliffs from the northwest, and dropkill the cage's lone guard.
You'll need to carry the prisoner out, so see to the the two guards at the northwest gate first. You can chainkill, snipe, or lure them over one by one.
Return to the cage and free the prisoner.
Carry him out through the just-cleared gate, and set him down once you're clear of the camp.
He'll relate how your contact has taken to a boat in Lake Moeris. Use Senu to tag it.
Catch up with him for a cutscene and an explanation. Not a good one- it seems like the Ptolemies would just threaten his family to lure him back in, plus using the ledger (as he intends to) woulddestroy his leverage, but then we're not here to judge.
He does also have a bulletin board for local quests, but these are all things that are already populated on the world map.
Head to your new marker in Euhemeria- you'll find Khenut there, probably cleaning up a trashed shop.
Speak with her and her daughter for the low-down.
The ledger is still their old house, follow Shadya there.
The place is being ransacked by soldiers. If you're looking for a stealthy approach, a good bet is the cliff east, which will allow you to leap straight to second level unobserved.
Still, sniping the third level lookout beforehand just seems to be a sensible precaution.
Jump over and stealth-kill the other soldiers on the second level. The last will be rooting around inside- you can surprise him by entering through the window.
Kill him and go downstairs. You marker will lead you to a desk and some scattered scrolls. Read the diary page for some chilling news.
Run back up the stairs and leap to the road. Your marker will take you to Khenut's shop, but the guards have already been by.
Follow the trail to the Euhemeria Lighthouse Camp.
You could swim or boat straight to Khenut by the lighthouse, but it'll save future complication by killing the small number of guards here right away. Plus, they probably deserve it.
When they're clear, talk to Khenut at the docks.
Senu will give you location a bit aways, and underwater. The fact that it's underwater gives you a bit of warning about what's to come. In one of the game's most depressing scenes, swim out and interact with the target to launch a long cutscene. When the scene ends, the quest is complete, leading straight into The Crocodile's Jaws.