After Said pleads to Tom Sheldon to assassinate Rico, he double-crosses Rico by complying with Said's pleas and places a hit on Rico for the Agency stating that he's "gone rogue".
The assassins are the Agency's agents being sent by Sheldon to kill Rico to prevent him from overthrowing Said so he can secure the US's interests.
They first appear in the mission "A good day NOT to die", a mysterious person radios Rico over the CommLink to meet in an alley in Kahnushahr, stating he has some information on Said's weaknesses. Rico is interested and decides to meet the Mysterious Person who turns out be an assassin. The assassin tries to unholster his pistol but Rico unholsters his own weapon faster and kills him. However, 4 additional men in tactical gear come out and point their weapons at Rico. They state that they were being sent by Sheldon to kill him and Rico is pissed. They engage Rico but and get killed by him.
Rico is enraged that his best friend has betrayed him, even screaming "SHELDON!!" he decides to find Sheldon and have "a little talk with him".
They are sent again in "Lister needs some help" where Rico is trying to smuggle weapons to the KRSL in a plane but black jets approach the plane from behind, they state again that they're being sent by Sheldon to kill Rico and start firing. Rico gets out of the plane in a stunt position and fires his rocket launcher at the jets, destroying them. Once the jets are gone, Rico pilots the plane again to meet Lister, with Lister questioning him on what those people are. Rico lies to Lister, saying he "pissed off some enemy a long time ago".
They're to seen again in "Kill Rico", where Rico meets some Corestar soldiers in a war-zone to discuss capturing an outpost near the war-zone only to interrupted by a sniper killing a soldier Rico was talking to. The soldiers fire at the snipers but are all killed by the snipers. Rico recognises them as Agency Snipers, and subsequently kills all the snipers and moves on to the outpost without Corestar assistance. He captures the outpost, but must defend it against The Agency who have operatives sent out to kill Rico. When that fails, they send a combat helicopter to kill Rico, but Rico destroys it and they retreat.
After mission 41, Said now thinks the Agency is incompetent and has Sheldon imprisoned. Rico hears of this and decides to rescue him. Parker questions his decision to rescue Sheldon rather than kill him but Rico mentions that he needs him as an asset to overthrow Di Ravello in Medici, where he was born. Parker accepts this answer and says that Rico has some "patriotic pride".
Finally, Sheldon and Rico have a talk at a cafe and Rico questions Sheldon about his motives but Sheldon admits that "he doesn't know". This annoys Rico but forgives him. However, he tells Sheldon that he's only doing it because he needs him for his departure to Medici. Rico also warns him never to do it again. He also mentions to Sheldon that he's done with the Agency after what they tried to do to him. He changes his outfit to that of Just Cause 3. He's officially quit the Agency. He never trusts Sheldon again after this mission, always accusing him of treachery and this continues in Just Cause 3. Especially with Bavarium on a Plane.
After the mission, the hit is called off by Sheldon and the Agency Assassins never appear again.
- This is the first time other Agency operatives are seen other than just Sheldon, Rico, and Maria.
- This entire plot line sounds very similar to the plot of the Jason Bourne film series.