What is the name of the modern-day protagonist in Assassin's Creed III?

Desmond Miles is the modern-day protagonist in Assassin's Creed III.

Desmond uses the Animus to experience the genetic memories of his ancestor Ratonhnhaké:ton, also known as Connor, during the American Revolution. His modern storyline continues the conflict against the Templars and the Abstergo organization that began in earlier main-series games.

Assassin's Creed III alternates between historical sequences and a contemporary plot involving Desmond and other members of the Assassin team. The modern sections also include exploration of locations such as New York and Brazil, along with missions connected to the approaching 2012 catastrophe.

William Miles is Desmond's father and an Assassin leader, not the protagonist. Layla Hassan becomes the central modern-day character in later games beginning with Origins, while Shaun Hastings is an ally and researcher. Therefore, the specific modern protagonist of Assassin's Creed III is Desmond Miles.