Modern day is now set in the 2090s. No mention of William Miles but presumably he would be dead of old age by now. Sean and Rebekah likely as well.
Basim/Loki apparently did *something* to both the Assassins and Templars in modern day that crippled both of them for a while. Basim is now searching for a way to reunite with his family thru different saints and other methods, but has moved on from extracting revenge on the descendants of Odin. Supposedly whatever he did to both the assassins and templars was to stop them from hindering his efforts.
The templars are using the AI in the animus to create “what if” scenarios to see if they can create another world ending solar flare so they can seize control. The AI animus is apparently letting them explore different options before being attempted in the real world.
The assassins are striving for historical accuracy to learn how to prevent the solar flares. Heavily implied Desmond and Layla are both now living AI gods of some kind inside the animus.