"Jackdaw isn't working alone; he's brought a new shadow organization to the game, and this is nothing short of war."
― The Financier mission briefing
Phoenix is a criminal organization created by Jackdaw with the only goal of destroying the organization he was almost assassinated by, Halcyon. They are located primarily in the United States, as opposed to Halcyon who are in Canada.
The organization is run from Chicago and possesses an extensive arsenal of weapons and equipment together with a number of trained operatives. Most major operations are coordinated by Jackdaw himself, usually with the Freelancer as their on-field operative.
- Black Dawn - Phoenix intercepts a returning team of Halcyon operatives.
- Halcyon discovered Rose was a double agent working for Phoenix, and thus Halcyon sent out Falcon to kill her near Erie.
- Dedication - Halcyon attempted an assassination of the Freelancer carried out by Wren, however Jackdaw saves them and Wren is killed.
- The Withdrawal - Phoenix robs one of Halcyon's banks in San Francisco.
- The Cache - After the death of Ryan Ross, Phoenix was not able to obtain the money on his offshore accounts so they set up a connection in the bank in Cincinnati, Ohio to recover the funds.
- The Scientist - Phoenix infiltrates a Halcyon safehouse in Canada to extract Rivera, a defecting scientist.
- The SCRS - Phoenix infiltrates a CSIS facility to obtain the schematics of Halcyon bunker they plan to attack.
- Jackdaw (Cutscene) - Phoenix prepares for their final strike at Halcyon.
- Black Dusk - Phoenix carries out a major assault against Halcyon. The Freelancer goes to one of their main, fortified bunkers and destroys it, however they are killed in the process.
- Epilogue - Jackdaw kills The Director, claiming Phoenix's victory in the shadow war. The organization is then disassembled, due to it completing the only goal it was made for.
- Phoenix is named after a bird in Ancient Greek mythology that cyclically revives itself.