On 16 December 2013, Nakamura was notified of the discovery of Milton Jones' ancestral ties to the Assassin Adéwalé by Dr. Damian Saravakos, revealing that while they may not find new artifacts in his memories, the genetic memory would be valuable to the employees at Abstergo Entertainment.
On 15 October 2015, Nakamura had a conference with Isabelle Ardant, and a year later was present during the initiation of Ardant's successor, Simon Hathaway, into the Inner Sanctum. Ten days later, Nakamura was among those who voted to clear Hathaway of all the charges brought against him, convinced by his speech and that his shady actions were in fact carried out for the benefit of the Templar Order
In March 2017, the Inner Sanctum invited the new Black Cross to a meeting in Quebec, during which Nakamura was present. Displeased that he auto-proclamed himself their inquisitor, they threatened him and demanded to know his identity. The masked man responded that he came only as a courtesy, to inform them that he was investigating an hostile fifth column within the Order. After affirming his independance, the Black Cross dropped a smoke bomb and disappeared. 
- Despite Mitsuko being a feminine given name of Japanese origin, in the non-canonical modern day storyline of the French Assassin's Creed comic series, Nakamura is depicted as a man and is responsible for giving the direct orders to the Templar agent Vernon Hest. Assassin's Creed: Heresy would later confirm that Nakamura is indeed a woman canonically.