The Dark Mirror project was a virus and the main plot device in Syphon Filter: Dark Mirror. Being a biological weapon, it was sought after by Red Section, who attempted to use it for their own nefarious endgame.
Considered a weapon of mass destruction by the President, the Dark Mirror was essentially Cochleanthes Amazonica gene-spliced with a member of the toxicondendron family. The resultant hybrid released an extract that could be synthesised into a devastating nerve agent. Unlike other nerve agents, which have limited lethality since they dissipate too quickly in the air, Dark Mirror in its aerosol form combined with oxygen molecules. This caused the gas to hover in the air for indefinite time frames. As such, Dark Mirror became even more lethal. If it was not for Addison Hargrove's interference, Red Section would have generated enough of it to kill half of Europe.
Dark Mirror was the main reason that Red Section assaulted the Alaskan facility of KemSynth Petroleum; the antagonists were searching for William Kreisler's brainchild, but they failed to acquire it due to the IPCA, which was sent in to perform a Precision Strike on the area. While carrying out his mission, Logan found requisition forms for hydroponics equipment, signed by Kreisler, and wondered why an oil refinery would require such instruments. In the process, Logan attempted to question Kreisler about the project but the scientist killed himself using a tropical flower. Gabe then found another similar flower deep inside the compound.
Eventually, Gabe Logan was redirected to the botanic headquarters in Iquitos, Peru, where he found Addison Hargrove, who was in charge of KemSynth security, being held hostage. He freed her and both recovered remnants of the Dark Mirror plant. When Lian questioned her, Addison told her she signed the forms because she was security commander. Lian goes on, asking her what is Project Dark Mirror and why Red Section wanted it. Hargrove counters that she wasn't involved in the research. She makes an excuse that her group found and cultivated rare plants, analysing them for their commercial value. She then claims KemSynth was apparently working on a new DDT, a miracle pesticide which would end world hunger. When Lian asks why Red Section would want a pesticide, Hargrove ignores her and leaves. Gabe lets Addison off, and tells Lian the NSA is following Hargrove, so they'll let the Agency know if anything happens.
While his partners investigated the plant material, Logan went into Bosnia, where United Nations were battling Zivmovic Prijateljstvo and Red Section. He rescued a private, Janzen, and tried to reunite him with his unit, but found that most of the members were dead. Gabe leaves Janzen and a wounded troop in the care of a soldier, Richard Kress after the latter asks him to recover medical equipment, but is ambushed by a ZP squad. This confirms his and Teresa's suspicions that Kress is in fact a Red Section mole inserted into UN forces posing as a medical officer. He hunts down Kress and kills him, avenging Janzen. He is then forced to confront Zivmovic, who hijacked an M1 Abrams main battle tank and came to help out Kress when the latter radioed for backup.
Gabe then headed into Kaliningrad, where MI6 was conducting surveillance operations on the Yavlinsky crime family. He acquired the recording devices that Maggie Powers had placed and uploaded the data to Lian Xing. While he did, he found yet another flower which Yavlinsky had kept, proving the antagonist was somehow tied to Red Section.
Following Gabe's investigation of Yavlinsky, Addison suddenly reappeared and asked for his help. When Addison made contact with him in Warsaw, Poland, Gabe realises she left the Agency because of a daughter, who Red Section had captured. She plays a tape where her daughter Blake, hurt by enemy forces, tells her to give them what they want. Questioning her further, Gabe learns KemSynth wanted Hargrove to believe it was a new DDT. She had doubts due to the tight security and hidden facility in Alaska. Logan decides to help Addison, but things take a turn for the worst when the latter attacks Touchstone, a member of Red Section. In retaliation, the antagonist kicks her off a railing and to her apparent death. Grief-stricken and infuriated, Gabe assaults Red Section forces and eventually confronts Touchstone. Although his most important weapon is stolen, Logan defeats the enemy and drops him off a mountain to suffer what he believed Addison experienced.
Gabe and Lian prepare for an assault on Red Section headquarters. The duo aim to secure Dark Mirror before Singularity, the enemy commander, can escape with it. Logan confronts his nemesis in a train station while Singularity, having hacked into Agency records, taunts him about his activities in the previous games. Gaining the advantage, Logan lets the antagonist mutter his last words and kicks him in front of a speeding train, finally ending the Dark Mirror threat.
Back at headquarters, the Agency analyse Dark Mirror and state their relief that the threat was neutralised. When Gabe visits Addison's grave a week after the AIT assault, he places a Dark Mirror flower on it. Hargrove appears behind him, telling him she faked her death with a cord tied to the railing. She and her daughter (the latter having indirectly revealed the fact that she's Gabe's child) then drive off because of Addison's refusal to let Blake live a life of violence.
Data that Gabe Logan recovered from Red Section headquarters found that Singularity had already reverse engineered the KemSynth data from the plants collected in Iquitos. Scientists under Red Section's employ had broken the genetic codes of the materials that KemSynth spliced into the plant. Mujari stated that the data in a computer Logan had found listed all of the splices which were designed to enhance the chemical reactions the plant extract had on the nervous system. As with any other nerve agent, Dark Mirror interfered with a nerve's ability to communicate. For instance, a heart would forget to beat, or lungs to breathe.