Markinson's first involvement with the Syphon Filter virus was after the botched operation in Guacimo, Costa Rica when Markinson found a way to contact Erich Rhoemer for the purposes of the Agency.
After Erich Rhoemer used 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 survives and woundsMara Aramov before finding out the bombs are in the Washington Park. With the help of CBDC, the bombs are disarmed and Logan takes out Jorge Marcos and Anton Girdeux.
Markinson sends Logan to the Pharcom exhibition center to investigate Jonathan Phagan's involvement with Erich Rhoemer but Logan discover that Edward Benton was working forBlack Baton and kills him. Logan tells Benton's betrayal 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 supposed death Markinson takes Logan out of the base before it explodes.
Markinson sends Logan to infiltrate Rhoemer's stronghold to inject some test subjects with a virus antigen. Deeper in the stronghold, Logan finds Jonathan Phagan who reveals that Lian is alive and she's infected with the Syphon Filter virus. When Logan talks to Lian she reveals there is no universal serum for the virus. 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 from the Agency. Lian analyzes the serum Markinson gave to Logan and discovers that the content was lethal and Markinson was having the test subjects killed. In the depths of the 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 off the edge of the walkway 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.
Markinson is briefly mentioned by Singularity, when he was talking about Gabriel Logan's past .
For most of the 1970s, Thomas Markinson was a soldier in the U.S. Army serving in Vietnam, where he received the Purple Heart and Medal of Honor awards. Following the end of the Vietnam War he worked with several intelligence fields in Washington, D.C. and joined the Agency as its new Director in 1997.
Markinson spent the last years of the decade running counter-terrorism operations against forces such as Erich Rhoemer's Black Baton organization. The Agency was under the influences of Vincent Hadden's international arms consortium, which used the intelligence group to aid in its activites. Markinson served Hadden and developed the notion to acquire the Syphon Filter virus for the Agency's uses. Together with Deputy Director Edward Benton, Markinson ended up employing Rhoemer after recruiting him in Costa Rica.
The Agency continued to assign Agent Gabriel Logan to the task of finding Rhoemer under Markinson's command, and Markinson manipulated Logan into destroying evidence of the operation. While in the Ukraine, Markinson supplied Logan with a serum of potassium chloride used in lethal injections to eradicate Rhoemer's test subjects and appear that he had vaccinated them.
Director Markinson was unable to control Rhoemer, who planned a terrorist strike with a Russian missile. He cut off contact with Logan and Lian Xing as the situation fell out of hand, and traveled to the PharCom warehouses in Kazakhstan to find Rhoemer. He confessed to his involvement in the Syphon Filter operation and his motivation for obtaining it to benefit the Agency. Rhoemer then shot him in the back of his head and caused Markinson to fall into the missile pit.
Personality and traits
Markinson is, while a reliable source of information during the attack on Washington, actually deceptive as evidenced by his claiming that Gabe is 'curing' the test subjects inside Rhoemer's stronghold by injecting them with an antidote when the truth is that he was having them killed with concentrated potassium chloride. He was also running a significant risk by having Benton, a mole in Rhoemer's ranks, work within the Agency. Despite all the help he gave Gabe and Lian, there was a side of him that was unknown, because with him dead, it would be impossible to find out his relationship with the terrorists.
- 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.
- The same trait is shared by Vince Hadden, who was the "Mystery Man" in this game, going into the second title and finally revealed in the third Syphon Filter game. He isn't killed by Logan, in fact he was to be arrested but Mara Aramov ended up killing him.
- Thomas Markinson is the only character in the whole game who never appears during the gameplay but only the full motion video cutscenes.
- Syphon Filter Briefing, viewed via pause menu (not the one before the mission) on Missile Silo level