In the year 1976, 23 years before the events of Shadow Man, Deacon had served in the NYPD Homicide Division. When investigating an abandoned New York tenement with his partner Gabe, they came across the Codex: an enormous and ancient tome that was sealed shut by a series of powerful clasps. Soon after, they are attacked by the Demon Sammael, who was also after the tome. In the struggle that followed. Sammael brutally kills Gabe and throws Deacon against a wall, badly wounding him. However, Deacon uses the tome to escape before Sammael could claim it and finish Deacon off. His legs had been broken in various places to the point where they had to be amputated and Deacon confided to a wheelchair for the rest of his life.
In 1999, during the events of Shadow Man, Deacon supplies Mama Nettie a case file containing information on five serial killers: Victor Batrachian, Marco Cruz, Milton Pike, Avery Marx, and "Jack 2" (John G. Pierce/Jack the Ripper). During his research, Deacon finds that all five had left particular notes at their respective crime scenes, which included symbols and poems that contained the phrase "for we are many" . This led him to believe that they were all in cahoots with one another which turned out to be true: all five were chosen by Legion to be the openers of the way, in which Legion's armies would cross the veil from the Asylum in Deadside to various locations in Liveside to commence the Apocalypse. These plans were of course stopped by Shadow Man.
In Shadow Man: 2econd Coming, Mike/Shadow Man meets with Thomas Deacon to learn about a symbol that was placed on Jaunty's head by the Bokor Papa Morte and a deceased person with the name "Morteth" written next to him. Deacon explains that Morte is Morteth, one of six Grigori and that his symbol is one of the seven signs of Evil, in which the star Wormwood sets high in the sky and the Grigori would reunite with their leader Asmodeus (the main antagonist of the game) and bring about Armageddon. Mike/Shadow Man is then sent to find a Sigil in the Plantation where Morte's territory is located. After returning the Sigil to Deacon, he explains that the area beneath the plantation is a Dark Sepulchre which houses a Recreant Vault that allows access to Gehenna, Asmodeus' hellish prison. Deacon then sends Mike/Shadow Man back there, giving him the Codex that would allow him to release Asmodeus from the Pit of Gehenna, once collecting enough Sigils and opening all seals on it, and given a Nephilem Shard that would allow Mike/Shadow Man to kill the Grigori. Deacon then also tells him of an item called the Grigori Chalice that can cure Jaunty of the Grigori curse. After this, he leaves his hideout in the Lafayette Cemetery in order to escape further detection by Morte's followers and would keep in touch with Mike/Shadow Man, "when the time is right".
By the time Shadow Man manages to free Asmodeus from The Pit in Gehanna, Deacon arrives in the form of an angel, prepared to fight the latter. Asmodeus then explains to Shadow Man that Deacon's true name is Deaketh, a Demon Malakim, one of his former foot soldiers , before the latter betrayed him. Deacon then attacks Asmodeus in his true form, only to be defeated. After Shadow Man fights and is successful in destroying Asmodeus, Deacon can be seen flying over Gehenna, stating that " the great dragon and his angels had been cast out".