In 1986, Mary committed suicide with the aid of her husband in order to prevent her capture by the Templars who sought to use her to locate an Apple of Eden previously handled by one of her Assassin ancestors. Holding Joseph's arm, she stabbed herself in the neck with his Hidden Blade and bled to death. After Mary's death, Joseph found himself unable to kill his and Mary’s son, and instead prompted Callum to flee before the arrival of the Templars led by Alan Rikkin. After Callum's departure, the heartbroken Joseph surrendered to the Templars and was brought to Abstergo Foundation.
Mary's death continued to haunt Callum for the next thirty years, the young child being unaware of his parents' allegiance to the Assassins and believing that his father killed his mother. Alone in the world, the orphan came to hate his father and later developed a deep hatred for men who attacked women. At some point before 2016, Lynch killed a pimp after he witnessed the man beating one of his prostitutes, a sixteen-year-old girl, and was sentenced to death by a jury due to his criminal record.
It was not until 2016, when the Templars faked Lynch's execution and brought him to their facility in Madrid, that he learned the truth about his mother. Informed about the Assassins by his jailers and having met with Joseph, Callum decided to help the Templars with finding the Apple to get his revenge on his father and the Creed for which his mother had to die. Eventually, Callum came to terms with the circumstances of his mother's death after exploring the memories of Aguilar de Nerha. Later, Mary mysteriously appeared among the crowd of Callum's Assassin ancestors who manifested themselves through the Animus after he fully synchronized with Aguilar. Mary spoke with her son, prompting the man to forgive his father and to pledge his allegiance to the Assassins' Creed, vowing to protect the Apple from the Templars.
- During the opening sequences of Assassin’s Creed: The Movie, Mary is shown to have died in 1986; however, later in the film, her name is shown on a genealogical board with her date of death marked as 1988.
- Mary inherited an Assassin medallion that was given to her ancestor by his lover, María, soon before her death.