The mastermind of this operation was Gabe Logan, who decided to end Mara's reign of terror once and for all which contradicted his previous choice of letting her retire in peace upon determining that Aramov was conspiring with Dr. E to further plot against innocent people.
Following The Omega Strain, Dr. E goes missing and leaves the Agency. In her depositions, she had admitted her intentions to change the world, and had met with Mihai Niculescu. Gabe Logan decides to put in a Discrete Personnel Elimination order for her and Mara Aramov; having always worked against the IPCA, Aramov had a significant role in manipulating Rhoemer, Hadden, even Niculescu, all the major players in the fiasco. To this end, Gary Stoneman is sent to neutralise the treacherous duo.
Upon setting up a sniper position in an apartment adjacent to Aramov's, Stone takes down her bodyguards and watches an argument between the two, who were secretly lovers. He kills the pair and then leaves, bringing the entire Syphon Filter incident to a closure.
- Mara uses a chair on her balcony in The Omega Strain's version of this event, but is strolling indoors in Dark Mirror.
- There are a trio of guards in Dark Mirror, yet in The Omega Strain Stone is seen zooming in on Mara, who is alone.
- Elsa Weissenger is absent from The Omega Strain's variant.