In 1986, he was taken by Abstergo Industries in their search for an Apple of Eden. In 2016, he was reunited with Callum and told him the details about his mother's death. Joseph was later killed during an escape attempt by other Assassins.
In 1986, Joseph helped his wife to commit suicide 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 departure, the heartbroken Joseph surrendered to the Templars and was brought to Abstergo Foundation. There, Joseph was put into an Animus but resisted synchronization with his ancestors, refusing to let the Templars discover the secrets of his bloodline. As a result, he suffered neurological damages and became blind.
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 Joseph 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 Joseph and his son were reunited. Desiring Callum's full cooperation, Rikkin decided to give him Joseph's old Hidden Blade and to let him confront his hated father. As Rikkin had foreseen and after hearing the truth from his father, Callum decided to spare Joseph and to help the Templars, to get his revenge on both his father and the Creed for which his mother had to die. Later, after Callum discovered the location of the artifact, the other prisoners mutinied in order to prevent the Templars from acquiring the Apple. Alan Rikkin then ordered the evacuation of the facility and the death of all the prisoners. Using the blade that Callum left to him so he could take his own life, Joseph killed a guard but was eventually overwhelmed and stabbed to death.
At the same moment, when a crowd of Callum's Assassin ancestors manifested themselves through the Animus after he fully synchronized with Aguilar, Joseph and Mary both appeared in front of their son. Nodding to them, Callum came to terms with the circumstances of his mother's death and forgave his father, making allegiance to the Assassins.
- Joseph Lynch is played by Brendan Gleeson and his son Brian Gleeson in the Assassin's Creed movie.