I am currently re-watching season 2 (yes, I know, I really should stop). In episode 2.2 "Trust Me," Irina Derevko turns herself into the CIA and Kendall pressures Vaughn to convince Sydney to talk to her. Vaughn explains to Kendall what affect this might have on Sydney, speaking with a woman she thought was dead, a woman who betrayed her, her father and their country. Vaughn looks to the TV monitor where Irina is pacing in her cell. Vaughn then says, “When she was done with my father, they could only identify him by his dental records.”
Vaughn learns later, in season 3, that dental records are not exactly solid proof of death in the world of Alias. Sydney is presumed dead, only after her dental records are matched with the remains found in her apartment after the fire. Sydney is, in fact, alive and has been the last 2 years. Could Vaughn’s line be another clue has to who is in a box? Could it be a clue years ahead of its time about his father and his father’s connection to Irina?