The Last of the Medjay (Main Quest)
This quest begins immediately after the death of Flavius, in The Final Weighing.
Journey back to Alexandria, to the place you first rejoined Aya.
A cutscene plays. Exit the cave, and follow your marker to Aya, on the beach.
Let the cutscene wash everything away, and complete the mission.
There's an epilogue with Layla in the real world. Though considering she just lived through the founding of the noble Assassins, had her best friend murdered by the opposition, and is under threat of death herself, she isn't very friendly.
You'll inevitably return to the Animus, but note that you can now read the tablet on the ledge in the main cavern here.
When you do go back under, it will automatically launch Fall of an Empire, Rise of Another.