Aten Rising (Main Quest)
Kick this one off by investigating a lead in the Temple of Karnak, on the northside of Thebes.
Getting anywhere near your quest marker will trigger a cutscene with the Priestess here, who tells you of some peasants that seem have reached a peace with their local demon-pharaoh.
Follow your marker out to fields, by Bebnum's House, and use your animus pulse to reveal the investigation points here. One is the central firepit.
One is the oil reserve.
One is the sun-dazed man near the firepit.
One is the chanting child.
And one is the kneeling man being menaced by soldiers.
When your investigation is complete, you'll get an objective to rescue the local priest from bandits. This will take you the Bone Picker Hideout.
Snipe the sparse bandit force from on high, then free the priest, and lead him out of the pacified camp.
Speak to him when you're well away from the camp, and he'll give you a mission to burn things. Specifically, things at the Cursed Farm.
Follow your markers to the three pyres and light them with your torch. Watch out for roving bandits and sporadically hostile vultures.
Return to the village at night, and follow the priest's instructions for the Aten Ritual (there is, incidentally, no way to palm any of the ritual silica for yourself).
Speak with him after for a clue about valuable intel in the Theban Archive
Scan the site with Senu, and enter through the hidden-passage-marked high window.
Clear any nearby patrollers, then go down the corridor until you encounter the pointing statue.
Follow his finger to the relevant scroll (you'll need to climb up the shelves a bit).
The scroll leads you to the pool of water at the Temple of Karnak's west end. Sunrise reveals the spot but you don't have to wait 'til then. Pulse-scan for gold marker, than dive in that direction to find a rotten wooden panel.
Bust through and investigate the gold markers. You may want to surface once for air, but remember you can fast travel underwater, if you need to.
When you've found the Aten statue and the tomb clue, return to the priestess Isidora, in the Temple of Karnak. This heated conversation completes the mission.