Conflict: Denied Ops is the fifth game in the Conflict series. Originally, the game was to be called "Crossfire" but was later changed.
The story takes place in a war where a Venezuelan conflict is taking place. General Ramírez and his associates have staged the Ramírez regime where Ramírez is slowly plotting to take over his country. First he sends his troops to seize the Petro Nivera Oil refinery then threatens to deploy nuclear weapons if the USA continue to "meddle in his country's affairs". Immediately two CIA operatives, Lincoln Graves and Reggie Lang are sent on a series of missions to take down General Ramírez and any other possible threat. First the two operatives are sent to the ruins of the Santa Cecilia monastery to retrieve important data on Ramírez's connections and associates. After extracting via their commander, they encounter a number of different conflicts all seemingly connected to Ramírez. Eventually they track down Ramírez and end up arresting him.
- Lincoln Graves: A former Delta Force operator and expert sniper. Graves is a highly disciplined operative but is not really the kind of partner for small talk or getting along with. His last partner was killed in Afghanistan in what Graves calls an "Occuputional hazard". Working with Lang, Graves does not like Lang's gangster like attitude in what he considers too noisy and undisciplined. Graves hides a dark past with Delta Force in which he doesn't want to share with Lang.
- Reggie Lang: The exact opposite of Graves. A rookie and newcomer to the CIA denied ops team, Lang likes to get the job done with explosives and a M249 PARA. Lang especially enjoys blowing stuff up. He however has a habit of calling Graves his bro, which annoys Graves. He also makes fun of Graves's age and jokes that he (Graves) was the sniper that killed JFK and numerous off color comments such as calling him "Whiteboy" and "Redneck".
- Dr. Alexander Pessich: A scientist who is forced to make nuclear bombs for Morchenko. Morchenko is holding Pessich's wife and daughter hostage. After being rescued, Pessich decides to redeem himself by disarming all the bombs he made and is extracted by Lang and Graves. His fate is completely up to the player. It is unknown if Pessich's wife and daughter managed to be rescued.
- Paul Foley: The Codex Red Team sniper who survived the ambush in Colombia in the previous game Conflict: Global Terror. He was one of the main four characters and he is a gulf war veteran in Conflict: Desert Storm and Conflict: Desert Storm II. He was traded by the drug cartel that captured him and is being held hostage by a Colombian arms dealer named Clay in Suriname. His fate is completely up to the player.
- General Ramírez: The mastermind of the regime. He stages a coup in his own country and the US intends to take action for his violent actions. In response Ramírez has his troops capture the local oil fields and threatens to deploy nuclear weapons quoting only "If the U.S. continues to meddle in his country's affairs". He is the primary target for both Lang and Graves to capture and the primary antagonist. He is captured at the end of the game.
- Abasi Atongwe: A rich African businessman and ruthless African rebel leader. When Graves and Lang are in Africa to determine the source of a transmission Atongwe somehow finds them and ambushes them. He is eventually tracked down to the ATAK Diamond mine and killed by the operatives.
- Alexsei Morchenko: A Russian brutish and thuggish merc. He supports the regime by forcing a doctor to make nuclear bombs for him. When Lang and Graves rescue Pessich, Morchenko is killed in the process.
- Clay: A Colombian arms dealer. He is seen dealing with Atongwe's lieutenant Kwennoir. He is also holding Codex Red Team sniper Paul Foley hostage. Clay is eventually killed.
- Jean-Baptiste Kwennoir: Atongwe's Lieutenant who deals with Clay. He is eventually tracked down and killed.
- Jacques: One of Atongwe's men. He is holding a Navy inspection team hostage on his ship and personally kills one of them in a cutscene. He is eventually killed by the operatives.