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Desmond, William, Rebecca, and Shaun find the Temple in a cave in New York and access it using their Apple of Eden. After partially activating the temple, Juno uses it to communicate with Desmond. Desmond is placed in the Animus where Juno's influence causes him to experience the life of his ancestor in 1754 England; the Templar Grand Master, Haytham Kenway.
Haytham assassinates a patron at the Royal Opera House and steals a medallion; the Key to the Temple's inner chamber. Haytham is dispatched to the American Colonies to locate the Temple. While in Boston, he kills a slave trader, freeing a group of Mohawks including a woman named Kaniehti:io. She helps Haytham find the Temple in exchange for him killing General Braddock. Haytham and Kaniehti:io find that the Key is not able to open the temple itself. The pair develop a romantic relationship during their time together. The perspective then shifts to Ratonhnhaké:ton's childhood in 1760. His mother dies during an attack on his village led by the Templar Charles Lee. Years later, the village Elder informs a teenage Ratonhnhaké:ton that their tribe's duty is to prevent the Temple's discovery. The Elder gives him a transparent Sphere which allows Juno to communicate with him; she tells him of his importance and shows him the Assassins' symbol. The symbol leads him to the retired Assassin Achilles Davenport, who reluctantly begins training him as an assassin.
Achilles suggests Ratonhnhaké:ton rename himself "Connor" to enable him to move more freely throughout the Colonies. While seeking supplies in Boston, Connor is framed by the Templars for instigating the Boston Massacre. Over the following years, Connor kills several Templars, and aids in the Revolutionary War between the Patriots and the British. Connor meets with his father, and the two forge a temporary alliance to eliminate a rogue Templar. Later, Haytham uncovers a letter detailing George Washington's plan to remove the Indigenous population, including Connor's tribe, from the frontier to prevent them supporting the Loyalists. Connor returns to his village and learns that Lee has recruited several Mohawk warriors to turn back the Patriots sent to eradicate them. Connor neutralizes the warriors to avoid conflict, but his childhood friend Kanen'tó:kon cannot be reasoned with and Connor is forced to kill him.
Meanwhile, Desmond is occasionally roused from the Animus to retrieve power cells from Manhattan and Brazil, necessary for activating the Temple, before the Templar Daniel Cross can take them. William goes after the final cell himself, but is captured by the Templars' modern day front, Abstergo. Desmond assaults the facility, kills Cross and Warren Vidic, and rescues his father.
Connor becomes conflicted about eliminating the Templars, and hopes to work with Haytham towards a common vision of peace and freedom. However, Haytham remains convinced of the chaos of freedom and the necessity to control the nation by replacing Washington with Lee. Lee is disgraced by Washington for attempting to sabotage the outcome of a battle and takes refuge in the heavily fortified Fort George. Connor infiltrates the fort and is confronted by Haytham; they duel, and Connor kills him. Connor later kills Lee and recovers the Key. With the Colonial Templars eliminated, Connor returns to his village only to find it empty, and the Sphere left behind. Using it, Juno instructs him to conceal the Key where it cannot be found; Connor buries the Key in the grave of Achilles' son, Connor Davenport.
In 2012, Desmond retrieves the Key and accesses the Temple's inner chambers. Juno informs him that activating the pedestal will save the world, but at the cost of his life. Minerva appears before them, opposing the plan as it will free Juno, who was sealed away in the temple to prevent her conquering humanity. Juno and Minerva explain that if the solar flare occurs, Desmond will be one of the few survivors in a post-apocalyptic world. After Desmond's later death, he will become revered as a god, whose well-intended legacy will be manipulated to control future generations, restarting the cycle. Desmond chooses to save humanity and give them the opportunity to fight Juno rather than be destroyed. William, Shaun and Rebecca leave the temple as Desmond activates the pedestal; a global aurora protects the planet from the solar eruption. Juno commends Desmond's choice and declares that it is time for her part to begin.
In the epilogue, Connor witnesses the last of the British ships leave New York and a trader selling slaves, a reminder that his fight for freedom is not over. Connor then returns to his village only to discover that the Mohawks have gone west after the newly formed Congress sold the land to settle war debts since, he is told, bringing in taxes so soon after a war fought to remove them would only serve to portray the newly formed US government as a continuation of its predecessor.
Following this, a modern-day voiceover can be heard directing the listener to locate a number of 'pivot points' that have been spread out across the memories' graphical representation of the Colonial America. Once collected, the voiceover returns to congratulate, and informs that they have now connected to the cloud.