Fighting for Faiyum (Side Quest)
This quest becomes available immediately after completing the Shadya's Rest side quest
Speak with the couple again, then go to follow up with the farmer that was being threatened by the captain.
He'll demur, saying he has to to burn all these pyres. Use your torch to help him out, but don't stand too close.
When you're done, speak to him and he'll relent, and vow to raise the locals. Return to the villa with the news.
Your conversation ends with Imperial soldier crashing in. They're heavies, but there's only three- you can dispatch them without even going downstairs.
Having reinvigorated Hotephres, it's time to team up with Khenut. Follow her to a rebel encampment in the bluffs.
The rebels cannot help you because their leader has been captured at the dam. Head over to sort things out.
The captain and treasure are both in the central tower, with a line leading down to the imprisoned rebel captain.
You can sneak in via the rope lines between the towers.
Kill the captain and loot the treasure from the red chest here.
This completes the location.
Note the arrows. You'll have to fight your way out of here, so you may want to do a little preparatory sniping beforehand. This includes the guy guarding the prisoner, who may be just a little too far away from the rope for a flying kill.
Slide down and free the prisoner.
Escort him south out of camp, fighting any remaining guards.
Safely outside, the leader will agree to help , and Bayek will head off to Fort Boubastos.
The Fort's a giant place, and halfway through rebels will attack, throwing a wrench into any careful plans, but there's still room for tactics. Do scan thoroughly before proceeding- it'll help you keep track of enemies once things go crazy. It'll also pinpoint the local treasures- three around the commander's quarter in the south building, one north near the not-quite-central watchtower.
Start at the north west edge of camp- there's a captain here you'll want to dispose of.
Some broken fencing in the bushes provides a good angle of attack.
Kill him and nearby enemies to get access to the underground tunnel across the way.
This leads to the prison area- you can either free the prisoners now (adding to the chaos, but probably getting most of them killed), or later (safer, but less helpful).
By this point, the rebel attack will have begun, but there should still be some high level targets in the area.
Keep stealth as long as you can, but once your cover's blown, use aerial attacks, smokescreen, and ambushes to keep the upper hand.
Keep at it until the enemy forces have been cleared. Be sure to use your adrenaline whenever it fills to speed the extermination process.
You can then recover the area treasures. The first is on the commander's table.
Note the large spiked door in this room. Two treasures are behind it, but you can't bust that door. Instead go out over the wall, and come at them from the other side, through what may or may not be stables.
Two chests are inside.
The last is just inside the door of that watchtower, on the ground floor. Snagging it completes the location.
Confirm kill the commander's body to advance the plot.
The power couple is waiting just a little outside the fort. Meet up with them again to complete the mission.
Also, they give you one of Shadya's dolls. Which seems… unnecessary.