In continuation to the events of Syphon Filter: The Omega Strain, Gabe sends a note to Mara Aramov. As she reads the note, a cracked scope appears from an adjacent balcony. It is quickly revealed that Gabe has sent Gary "Stone" Stoneman to kill Mara due to her manipulative role in the Syphon Filter conspiracy. Also revealed is a private meeting between Mara and Elsa Weissinger, who was conspiring alongside Mara. Two years after Aramov and Weissinger are killed by Stone, Gabe from the International Presidential Consulting Agency (IPCA) is sent to Kemsynth Petroleum in Alaska. A paramilitary group known only as Red Section has taken the complex. Upon heading into the Kemsynth facility, Gabe comes across and kills Red Section members Red Jack and Black King. Before Gabe could rescue any living hostages, two of them, Kreisler and Freeman, commit suicide. A data disc reveals that the attack is connected to Kemsynth's botanical arm in Peru in charge of making a new pesticide. The IPCA also learn that a former Agency operative, Addison Hargrove, who was Gabe's first partner romantically and professionally, is in charge of security. Gabe enters Peru to find the rebel forces allied with Red Section destroying Kemsynth's laboratories in Iquitos. Upon searching the area, Gabe saves Addison from interrogation by a Red Section member, Black Viper. Prior to their escape, the pair discover and retrieve samples of the rare plants found on Kreisler and Freeman before being ambushed by Red Section member White Scorpion. Gabe and Addison manage to kill White Scorpion and his henchmen, only for Addison to disappear after extraction. The recently gathered intelligence leads Gabe to a weapons factory in Bosnia. Like Peru, a group of local rebels have been aided by Red Section. Here, Gabe saves a UN soldier, Private Janzen. Gabe tries to reunite Janzen with his squad, only to find they have been slaughtered. The pair meet up with Kress, a Red Section mole posing as a UN medic. Janzen and a wounded soldier are murdered by Kress while Gabe survives an ambush by rebel forces. Logan kills Kress and the rebel leader, Goran Zimovic. An upload of Kress's files from his laptop reveals the names of Red Section leaders: Touchstone and Singularity. Gabe heads to Kaliningrad where his MI6 counterpart has installed recording devices in a casino serving as a Yavlinsky crime family front. While in Yavlinsky's casino, Gabe discovers that Niculescu formerly laundered weapons and cash to Red Section and that Mara was an assassin hired by Yavlinski eight years ago. After dealing with Victor Yavlinsky and his security forces, Gabe finds the MI6 recording devices and leaves the casino, killing Red Section forces in the process. Gabe meets Addison in Warsaw where she tells him the reason she left the agency: she had a daughter whose name was Blake. Gabe tries to find out whether he is her father but Addison persuades him that he isn't because Blake is only ten. Blake was kidnapped recently by Red Section to make Addison give them what they want. The deal is for Addison to meet Touchstone, the second-in-command of Red Section, at TransEuro Tram station in Germany and turn over the disc containing information on Project Dark Mirror, the one she stole from KemSynth office in Iquitos, in exchange for Blake. Addison began having doubts about KemSynth creating a new DDT and tells Gabe she doesn't want to hand over the disc to Red Section. They made a plan: Addison would provoke Touchstone into talking by bargaining with him while Gabe would take Touchstone out. They attempt the exchange. However, Addison discovers Touchstone brought snipers with him. After failing to drive Touchstone into a bargain, Addison starts fighting with Touchstone. He kills her by pushing her over the railing into the valley. Gabe feels guilty and sorry and he fills up with fury and rage. He decides to complete Addison's last wish: save her daughter. He chases after Touchstone and defeats him. Prior to Touchstone's death, Gabe tells him that nobody chooses his death and throws Touchstone into the abyss. After the confrontation, Gabe learns how Red Section was formed, and Singularity's real identity, Grant Morrill, an Interpol accountant who disappeared and started his own company, Aeroscience Integrated Technology (AIT). Gabe and Lian head to AIT to end Red Section's future operations and save Blake. Inside AIT, he learns that Singularity developed electromagnetic Kevlar armor which deflect projectiles, except those from electroshock weapons. Gabe and Lian succeed in rescuing Blake, while Singularity hacks into IPCA's files. Gabe confronts Singularity in a bullet train station. Singularity has built canisters of the element known only as Project Dark Mirror, a nerve gas that could kill millions by fusing with oxygen molecules. In the battle, Singularity provides his complete "review" of Logan's previous operations, and further taunts Gabe that they are the same. After uttering his last words, Logan kicks Singularity in front of a moving train, which kills him. Logan reunites with Blake and Lian. Gabe heads to Addison's plaque at Arlington National Cemetery a week later and leaves a flower, the same flower Singularity used to genetically engineer the nerve gas Dark Mirror. Addison re-appears behind Gabe, telling him that she faked her death. She prepared her death in advance and tied her self with a bungee cord to the railing. Gabe is upset that she once again lied to him. Blake comes inside and greets Gabe. He honors her as the bravest ten-year-old he's ever met. She corrects him, by saying she is twelve, not ten. Addison left him, and the Agency, twelve years ago because she was pregnant with his child and didn't want her involved. Gabe attempts to tell Blake the truth about himself, but is stopped by Addison, who states that Gabe will never want to leave the Agency, and that he could end up causing indirect harm to Blake. Gabe reluctantly lets them leave. A bonus level in Bangkok takes place after the AIT assault. Jimmy Zhou, a gang leader tries using the avian bird flu as a weapon against his rivals. Gabe kills the birds and learns that Zhou has taken Lian hostage. Inside his penthouse, Gabe faces an army of Zhou soldiers, including one with a Gatling gun. Gabe manages to rescue Lian and kills Zhou.