Jonathan Hawk is a member of the Assassin Order and a descendant of the Aleman Assassin Accipiter and Egyptian Assassin Numa Al'Khamsin. In 2012, he went into the Animus to relive the memories of his ancestors. He was a member of the Assassin cell based in London, headed by Stella Crow, of which Nancy and Steve were also members.
While in the Animus, Jonathan lived through the memories of his ancestor Accipiter of the Battle of Mediolanum in 259, between the Alemanni and the Romans in Aube. After spending a while longer with Accipiter's memories, Jonathan's nurse unplugged him from the Animus to let him rest for two hours, as longer sessions could be dangerous for his mental health.
Due to an 'incident in the field', Jonathan had lost his right eye. To remedy this, he went to see professor Terrence, a professor specialized in 'optical technology', who proposed to execute a revolutionary transplantation: a miniature camera was to be implanted in his eye socket. Although Jonathan's artificial eyeball had been stolen two days earlier, the operation did not have to be postponed. How the thieves had proceeded and what they attempted to achieve was unclear; the eyeball, after all, was unable to function on its own.
The conversation was then interrupted by a phone call from Stella Crow. Jonathan was subsequently instructed to go to Monteriggioni, Italy to gather all the information collected by Shaun's team. Jonathan's team particularly wanted File 24 – a dossier about the Scepter of Aset – which had been already sent to Desmond Miles.
After three days, Jonathan arrived in Monteriggioni and asked his fellow Assassins for the "Folder Nº24". In the process, he discovered he was a distant cousin to Desmond and, upon looking at the folder, Jonathan noticed a picture of an Egyptian pyramid, quickly realizing where his mission would take him next. The folder also contained information about the Scepter of Aset.
Jonathan and the other Assassins discussed the purpose and power of the artifact. At last, Lucy Stillman gave Jonathan the Ankh they had retrieved and she told him that Stella could ‘meet’ her ancestor Lugos through the artifact. The Assassins then wished each other luck, with Jonathan returning to his cell based London.
Back in London, Jonathan relived the memories of Numa Al'Khamsin, an Egyptian Assassin who came in contact with the Scepter. However, while he was in the Animus, Jonathan suffered a stroke, due to his low tolerance of the machine, and was escorted to the emergency room. The incident had happened due to Nancy, an assistant, having made a mistake while installing the timer, causing it deregulate and expose Jonathan to the Animus for a longer period of time than usual. Stella severely reprimanded Nancy, kicking her off the team and even threatening to consult the other cells in order to expel her from the Brotherhood.
While Jonathan was unconscious, Steve, a Templar mole, saw the chance to kill him by removing his oxygen mask. However, Jonathan survived and confronted Steve, who was already being held at gunpoint by Nancy and Stella; they too had discovered Steve's defection to the Templar cause. Steve then tried to flee, but Jonathan chased him down and killed him.
Jonathan continued his Animus sessions, but was given more breaks as a precautionary measure. During one such break, he and Nancy had a profound conversation about their relationship. Nancy was in love with Jonathan, but he thought it was a bad idea to "fall in love with a soldier". Nevertheless, the two kissed, but were interrupted by a phone call from professor Terence; Jonathan would undergo the transplantation the next day.
The transplantation was successful; although he could not use his left eye anymore, his new camera-eye improved his eyesight and field of view significantly. Returning to his Assassin cell the following day, Jonathan wished to return to his Animus session immediately and continue the search for the Scepter of Aset.