Charles Lee is the main antagonist in Assassin's Creed 3.
Historically, he was a British general who sided with the rebels when the revolution broke out. He later left the rebellion after George Washington was made Commander in Chief.
Role in Assassin's Creed 3
Charles Lee is introduced as a sympathetic character at first, helping Haytham Kenway in his quest to find the precursor vault. He serves Kenway's order until he's accepted into the group, at which point it's revealed that Kenway is a Templar and Lee is made a Templar.
Several years later, Lee runs into a young Connor near Connor's village. He nearly strangles the boy whilst interrogating him as to where his village is. Connor makes a point of remembering Charles's name as to later find him and kill him. Lee then proceeds to burn down Connor's village, killing Connor's mother.
Years later, Lee is now second in command under Haytham. He appears during many historical events and orchestrates the Boston Massacre. He also oversees the Boston Tea Party. He sides with the British at first but ends up joining George Washington. He's there for the signing of the Declaration of Independence in Philadelphia where Connor almost kills him.
Lee hates the fact that George Washington is Commander in Chief, Charles, as well as the rest of the Templars, believe that Washington should be assassinated and that Charles Lee should lead the revolution. Lee orchestrates an assassination plot, where he frames Connor for the murder of Washington. Connor barely stops the plot after spending multiple days in prison, but Lee gets away.
Lee is ousted as the perpetrator of the plot and is banished by Washington, which frustrates Connor who wants to see him dead. It's also revealed that it wasn't Charles who burned Connor's village but Washington, in an effort to keep the natives from cooperating with the British. This changes nothing for Connor who still wants to see Lee dead.
Towards the end of the game, Lee isolates himself in a fortified military district of New York. Connor has the district shelled in an effort to reach Charles but Lee escapes the shelling when Haytham warns him about the plot against his life. Haytham also gives Charles the precursor relic that Desmond is looking for.
Connor tries to assassinate Lee during Haytham's funeral. The plot fails but this makes Lee paranoid and he tries to flee New York by ship. Connor hunts Lee down, critically injuring him. Losing massive amounts of blood due to a gunshot wound, Lee retreats to a small pub in the middle of the forest where a wounded Connor finds him, shares a drink with him and stabs him in the chest, ending his life.