The Kazakhstan Missile Incident was a major confrontation of Syphon Filter wherein Gabe Logan attempted to stop the Black Baton leader from launching a missile at his target. It involved numerous parties, including PHARCOM security personnel, Rhoemer's thugs and the Agency.
The conflict was significant, causing most factions to suffer from substantial losses. In the chaos, Thomas Markinson was killed by Erich Rhoemer, who then fell victim to a gas grenade which Gabe Logan threw at him. Black Baton was then terminated or disbanded, as was PHARCOM. Gabe Logan then called in the CBDC to secure the area and acquire Phagan's data when the ordeal ended.
"Rhoemer's men... Phagan's men... it's a warzone down there."
"The mainframe's in a silo beneath the abandoned warehouse. The only way in is through a series of mining tunnels. Warehouse 76 has an elevator that goes down to 'em.
Once in the silo, you'll need a series of keycodes to operate the computer. You have to get that from Richard Erikson. He's in charge of PHARCOM's European operation, so he must be down there somewhere."
"Where can I find him?"
"Phagan was in the process of moving the shipping office, but it used to be on the second storey of one of the warehouse."
"I need to tag all the viral carriers down there so nothing slips through the cracks. How many bodies are down there?
Interrogating Richard Erikson
Deactivating the electric fences
Reaching warehouse 76
Reaching freight elevator
Shutting down power
Rerouting elevator power
Finding missile silo
Recovering missile destruct code
Preventing World War III
Logan vs Rhoemer
"Logan!... Don't you know when to quit? We'd have made a great team."
"I don't think so."
Infuriated at Gabe's interference, Rhoemer makes his presence known and engages the operative in a final showdown. However, Gabe defeats him with a gas grenade and brings the Black Baton organisation to its knees.
"As many of you already know, four hours ago a nuclear missile detonated over Kazahkstan. The Kazahkstan government assures us that this was an accidental launch and that the missile was destroyed via their own safety countermeasures. An investigation is underway."
-Vince Hadden reports a cover-up of the event during Syphon Filter 2
With the crisis narrowly avoided, Gabe calls in CBDC forces to secure the area and resolves to get Lian's vaccine. Mara Aramov would establish her first contact with Vince Hadden, seemingly the Agency's commander, while the latter would then announce how a third world war was imminent but did not materialise.