As top security personnel, McGowen was present throughout the Animus sessions Sophia conducted in late 2016 on one of her subjects, Callum Lynch, in search of the Apple of Eden recovered by Callum's ancestor Aguilar de Nerha. In one of these sessions, he expressed to Callum his admiration for the Assassins, particularly the Levantine branch of the 12th century. The popular story of the Assassins deriving their name from hashish and their use of the drug to reinforce commitment resonated with him; he was unaware that this tale was actually fabricated by the Assassins' enemies during the time of the Third Crusade.
After the Assassin subjects, along with Callum, broke out of the Madrid facility, McGowen accompanied Alan Rikkin, CEO of Abstergo Industries, to Seville for the retrieval of Aguilar's Apple of Eden from the tomb of Christopher Columbus. He then followed Alan to London for an assembly with the Templar Council of Elders, where Alan was to present his newly acquired Apple of Eden.
This assembly was interrupted by the Assassins who had escaped from Madrid. In spite of his Assassin sympathies, McGowen was devastated when Callum killed Alan Rikkin just as the latter activated the Apple of Eden before his audience.