Markinson sends them on a mission to find the viral bomb in Washington, D.C, where Erich Rhoemer & the Black Baton lead a assault on the city. Logan finds a fake main bomb at a subway, leading to a explosion, he find & wounds Mara Aramov and Markinson orders him to find the bombs in the Washington Park. the CBDC disarms them everywhere.
Logan heard that Edward Benton was working for Black Baton in a exhibition center, he heads there to find Benton, and kills him. And interrogates Markinson on the way out. He takes Logan to Rhoemer's base in Kazakstan and while planting the bombs on every gasoline tank, he kills Gabrek. And the base is destroyed while him & Markinson make a getaway. While Logan picks up communication from Lian, she is now taken hostage by Rhoemer. And sent his attack chopper to kill him. he escapes again.
Markinson sends Logan to infiltrate the stronghold to inject some patients with a antidote. Deeper in the stronghold, he found Lian alive and she's infected with the Syphon Filter Virus. Markinson is negotiating secretly with Rhoemer for the Syphon Filter virus to the Agency. while Logan makes his way to Rhoemer, he meets with Markinson on a walkway near the missile and both begin to talk about the virus.
While monologuing about the missile and how Logan has no idea what things are going on, Markinson is violently shot in the back of the head by Rhoemer and falls of the edge of the walkway and falls to the bottom of the missile launch site where he lands dead in the bottom of the missile, never to be seen again. At the end of Syphon Filter Lian asks Logan what were they working for and what were Markinson's ambitions, all Logan knows is with him gone they may never know.
Although not making any appearances, Logan mentions him at certain points in the game, especially when he is communicating with The Agency or talking about it.