Deacon first appeared inthe Tutorial, where he confronts the player, Boochbeard, Mr. Gandy, and the starter companion. The starter companion states that Deacon was the player's jailer, and he will pay for hurting him. He calls in Battle Angels to deal with the player. However, He/She defeats the Battle Angels, but Deacon will then summon a squad of Dragoon clockworks and then tells the player and the first companion to surrender or be destroyed. But Boochbeard fires a flare into the sky and his ship's cannons destroy the Dragoons. Deacon then says the quote " Hmm. Impressive. It seems we have underestimated you, young pirate. You'll regret making an enemy of the Armada. Enjoy your freedom, while it lasts". Deacon then uses a hidden gun and shoots an explosive near Boochbeard, nearly killing the latter and then uses the opportunity to escape in a puff of smoke. At this point most players will realize that the armada is quite powerful.
The war and its aftermath was a wild, lawless time in the Skyways. Colonies, cut off from their owners, collapsed into anarchy or fell to hostile raiders. Mercenary ship captains constantly switched allegiances, fighting for Marleybone this week and Polaris the next, switching flags whenever the winds of profit and fortune changed. In time, some of these captains refused to follow any nation- they saw the ships of every side as prizes waiting to be pillaged. Though even when profit was available for people with such skills some of these people still resisted the law. Luckily law enforcement was poor in the polarian war. Then were the pirates were truly born.
Pirates flourished in the outer reaches of the Spiral, where the colonial powers spread their forces thinner and thinner. In Skull Island, gangs of Pirates took control of entire Skyways, building their own ports and cities and launching daring raids in every corner of the Spiral. After the war's end, the great navies had been humbled and broken- no one could stop the spread of piracy and the Pirate lords amassed huge hoards of plunder and gold. Captain Avery dreams of transforming Skull Island from a den of thieves into a new Pirate republic. This is the Golden Age of Piracy, when Wharf Rats and Cutthroats can make imperial navies tremble.
But, of course, the Armada hated pirates and resolved to find and kill them all. Deacon, the Spymaster of the Armada, who is in charge of capturing pirates, encounters the player during the tutorial (the prison break by Mr. Gandry and Boochbeard). You eventually escape as you defeat the Clockwork henchmen when Deacon escapes, but your objective will be to stop the Armada from hunting down every pirate. Along the journey, even into Valencia itself, you will meet Deacon working with other crooks on numerous occassions, including the Duck of Death (Cool Ranch), and Bonnie Anne's second promotion.
Deacon tracks you into Captain Barnabus Blood's lair and you finally defeat him in a massive battle for Blood's treasure, and the second piece of Marco Pollo' s map. However, he is finally destroyed in the battle.
Another thing, the Player must find the pieces of the map of Marco Pollo's treasure, the original objective of the quests which will lead to deadly encounters, among them General Tso, Doctor Noh, Ike Bronco, the dreaded Captain Blood and even Rooke, Supreme Commander of the Armada Troops, who wants to get revenge on you for defeating his brother!
He and Rooke were rebuilt by kane later on. Kane states that Rooke and Deacon were simply "machines", and they could have easily been replaced. They are also slightly stronger than they were before. Both Rooke and Bishop have the same abilities as before. Rooke can still deflect any hit from a Musketeer. However, the player and his crew easily deal with the Armada Elites, leaving their carcasses in the machine core. This time, Rooke and Deacon are probably permanently finished, but who knows.