Their Benefactor
This is more about The Lost Codex than the finale. Okay so Veritas' Benefactor was a high ranking member or Dorna, who was actually a traitor to Dorna because he was secretly funding Veritas to prevent Dorna doing what they do.
Now at the end of The Lost Codex their Benefactor get the plans to that device and puts it in a room with a whole bunch of Da Vinci's things. Now in that scene i get the feeling your supposed to have seen something that should have shocked you. Forgive me put i couldn't pick up on what that might have been - i think it's something to do with the Portrait.