Markinson first involvement with the Syphon Filter virus was after the operation in Guacimo,Costa Rica when Markinson find a way the contract Erich Rhoemer for the purposes of the Agency.
After Erich Rhoemer using his criminal organization Black Baton to lead a assault on Washington, D.C, Markinson sends Logan and Lian on a mission to find the viral's bombs planted in the city. Logan finds a fake main bomb at a subway, leading to a explosion, he find & wounds Mara Aramov and find out the bombs are in the Washington Park. With the help of CBDC, the bombs are disarmed and Logan take out Jorge Marcos and Anton Girdeux.
Markinson sends Logan During Phancom exhibition center to investigate Jonathan Phagan involvement with Erich Rhoemer but Logan discover that Edward Benton was working for Black Baton and kill him. Logan tell's about Benton to Markinson only to be surprised when Markinson says he knew it all the time. Markinson takes Logan to Rhoemer's base in Kazakstan and while planting the bombs on every gasoline tank, Logan kills Vladislav Gabrek. After Lian's suposed death Markinson takes Logan out of the base before it explodes .
Markinson sends Logan to infiltrate in the Rhoemer's stronghold to inject some Test Subjects with a antigen. Deeper in the stronghold, Logan with the help of Jonathan Phangan, Logan found out that Lian is alive and she's infected with the Syphon Filter Virus. When Logan tells about the serum to Lian she reveal's there is no universal serum for the virus, then what he was injecting those men was not an antidote,and that Markinson fooled Logan about the serum. With the help of Mara Aramov, Logan and Lian go to PharCom's warehouses in Kazakstan to prevent Rhomer's ambitions to launch a missile to cause a third world war, there they lose all contact with Markinson and anyone of the Agency and Lian analyzes the serum Markinson gave to Logan and discovers that your content is lethal and Markinson was having the Test Subjects killed. in the depths of Silo Logan encounters Markinson on a walkway near the missile and both begin to talk about the Markinson involvement, when he reveals that his goal was to get the virus to the Agency.
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.
He is however mentioned in conversation between Vince Hadden, Lyle Stevens, Mara Aramov and Mr. Cochran. Mara tries to use Markinson against Stevens in their argument, saying a lot of their current problems was due to his actions. Stevens remarks that first he's not responsible for the actions of his predecessor and that Markinson was "not in control" (of the Agency). Hadden then begins to proceed to question Cochran, staying that "unlike Markinson and Rhoemer, you have failed"...before Mara snaps Cochran's neck.
- Despite being the secret antagonist of the game, he is never actually faced in combat and Gabe does not kill him. It's uncertain if Gabe would have killed him anyways.
- ↑ Syphon Filter Briefing, viewed via pause menu (not the one before the mission) on Missile Silo level