After Mara Aramov and Elsa Weissinger are assassinated by Gary Stoneman, Gabe Logan from the IPCA is sent to Kemsynth Petroleum in Alaska. A paramiltary group known only as Red Section has taken hold of the complex. Upon heading into the Kemsynth facility, Logan comes across a Red Section lieutenant codenamed Red Jack, a soldier who bears a striking resemblance to Anton Girdeaux in terms of body armor and weaponry. As with Girdeaux, Logan is able to kill Red Jack, and heads down to the lower shaft to investigate further. After finding clues that prove that Red Section is searching for something, Gabe faces off with the RS onsite commander, Black King, a heavily armed soldier that is the apparent leader of the attack. He arms electronic explosives to destroy the factory, but Lian draws his fire and Logan deactivates the bombs. His hostage, Malcolm Freeman, commits suicide by swallowing a cyanide pill. Another hostage named William Kreisler also kills himself by sniffing a poisonous plant that Logan finds on his body.
A microfilm reveals that the attack is connected to Kemsynth's botanical branch in Peru in charge of making a new DDT pesticide. They also learn that a former Agency operative, Addison Hargrove, Gabe's first partner, professionally and romantically, is in charge of security. Gabe goes there to find the rebel forces destroying Kemsynth's labs in Iquitos, only to find that they are in ties with Red Section. Upon searching the area, he comes across his former partner being held captive for interrogation by a Red Section sergeant codenamed Black Viper. While questioning Addison, Black Viper remains unaware that someone else is watching, and Gabe assassinates him through the curtains. Upon attempting to escape, however, Addison and Gabe discover more of the rare plants found on Kreisler as well as Freeman. When they retrieve samples of the plants, they are ambushed by multiple rebel personnel. Gabe hijacks a turret which a soldier was using, and mows them all down to protect Addison. As they try to leave, a Red Section lieutenant, White Scorpion finds them after Black Viper didn't report back to him, and attempts to kill both of them using the same turret gun Gabe was in control of. Logan eliminates White Scorpion with his MB150 sniper rifle, and manages to get Addison home safely, only for her to vanish from him once more.
From their information, Gabe heads to war-torn Bosnia to find another revolutionary organization, this time in an embattled weapons factory. As with Peru, these soldiers are receiving aid by the ruthless Red Section. Here, Gabe rescues and meets a young UN soldier, Private Janzen. Gabe tries to reunite Janzen with his group, only to find they have been slaughtered. Along the way, they meet up with Richard Kress, a UN soldier who tells Gabe to find some medical equipment to help a soldier that is in serious need of help. Logan leaves Janzen as well as the injured trooper in Kress' care; but when he finds the cabinet Kress was talking of not only is it empty, he is also ambushed. After killing the rebel soldiers he find Janzen and the wounded soldier murdered while Kress is gone, proving Kress was a Red Section mole posing as a medic in the higher ranks of the UN. He finds Kress ready to escape and, while taunting the mole, kills him. He faces down the rebel's sadistic leader in a hijacked M1 Abrams UN tank and uses a SMAW Anti-Tank to destroy the tank thus killing the leader, Goran Zivmovic.
With Addison mysteriously gone, Gabe goes to Kaliningrad where his MI:6 counterpart has installed micro recording devices in a casino serving as a Yavlinsky crime family front. Gabe finds a prostitute being beaten by one of Yavlinsky's men (The dead body of a prostitute found outside the casino suggests the guy is a serial killer). He rescues her by killing the mafioso.
It is learnt here that before the Syphon Filter fiasco, Mara took a job from this crime family to kill rival criminals on Christmas Eve. She left the bullet casings in their kid's stockings. She also sold Niculescu's paintings on the black market as her source of income until she died. While in Yavlinsky's casino, Gabe discovers that he was using the casinos to launder both weapons and cash to Red Section. After dealing with a significant amount of Yavlinsky's security forces, and eliminating Victor Yavlinsky himself, Gabe finds the MI:6 recording devices then calls it done. Before he can leave, Red Section personnel storm the casino, along with one of their two elite leaders, Touchstone, who kills Yavlinsky's lieutenant for their failure, then orders Red Section troops to eliminate every bit of information that could be leaked about his deal with Yavlinsky, thus killing any survivors in the casino in the process. Logan takes them out first, then escapes with the MI:6 recording devices and Lian.
Gabe meets up with Addison in Warsaw, Poland. Here he learns the truth about why she left Gabe and the Agency twelve years ago. She was pregnant, and she did not want her daughter, Blake, now ten, to be raised in a life of violence. Despite this, Red Section tracked down her daughter's boarding school and captured her. They send a video tape demanding that Addison meet Touchstone, the second-in-command and Red Section head of security, and turn over her data discs containing information on the mysterious Project Dark Mirror to him. In return, she will get her daughter back. However, Addison's experience has taught her that Red Section is ruthless enough to kill Blake anyway, as the ransom tape, has audio of Touchstone forcing her to cooperate. They also send Adddison Blake's left tennis shoe.
They meet at a tram terminal in the German Mountains of Zugspitz Pass. Touchstone brings Red Section guards to the meeting spot and as he quarrels with Addison, she hits him. Touchstone shoves her over the railing and she falls off the mountain to her apparent death. Gabe is distraught that he failed to rescue her and becomes obsessive in single-handedly destroying Red Section. Gabe believes in controlling one's destiny over Addison's belief in fate. He rescues hostages inside the transport atrium area, and becomes hell bent on killing Touchstone. Upon reaching the transport ski lift area, Touchstone comes up from behind, and beats Logan down, then steals his MB150. Even after using Logan's most important weapon, however, Touchstone is beaten, and dragged near the edge of the mountains. Logan then holds Touchstone overboard, ready to drop him off as they share a few choice words with one another. Touchstone then tells Logan to die well, as he is dropped off the mountain to his death.
Gabe learns the truth behind Red Section. Grant Morrill was an Interpol accountant who audited and copied multiple information sources he had so he could disappear and start his own company, Aeroscience Integrated Technology (AIT). Mild-mannered Grant Morrill became the sadistic, almost sociopathic entity known only as Singularity, one of the most disturbing characters Gabe has ever faced. Additionally, considering he has dealt with Erich Rhomer, Mara Aramov, Mihai Niculescu and Jason Chance in the past, this would be a great challenge to Gabe. However, learning that an accountant was behind all of this makes Gabe furious, more apathetic to Red Section, and it consumes him unlike anything he ever faced in the Syphon Filter conspiracy. He and Lian go to AIT to stop Red Section once and for all, and to rescue young Blake.
Inside, he learns that Singularity has built a new type of technology: an electromagnetic suit that deflect all kinds of bullets. Despite its advantages, an electric weapon can disable it long enough for Gabe and Lian to do some damage. Lian goes to rescue Blake, who is trapped in a rising pool of water. Lian feels that she is emotionally drowning because Gabe has never obsessed about her. What she does not know is that Gabe did obsess about her in Syphon Filter 2 (the second season) when she was infected with the Syphon Filter virus. Lian succeeds, but Blake runs away. Gabe tracks her down to a centrifuge room, where she has been taken hostage again. Gabe kills the Red Section soldiers holding Blake, still with only one shoe, and teams up to stop the centrifuge so Lian could rig a bomb to it then use it to break down a door. Singularity hacks into IPCA's Zeus Files to taunt Gabe. Gabe enters, takes down two EM guards and storms the bullet train station. Singularity has built canisters of the element known only as Project Dark Mirror. Singularity is in a EM suit stronger than the other EM suits, similar to the Emergency Defense Squad-Unit One full body armour suits but not as strong as Jason Chance's ultra-tough body armour in SF2, which was even impervious to M-79 grenade shots. In the battle, Singularity provides his complete "review" of the Syphon Filter attacks, from mocking him about those who repeatedly betrayed Gabe from the Georgia Street subway bombing to the Niculescu obsession and Stone's involvement in IPCA.
After killing the other soldiers, Gabe allows Singularity to say some final words as he is held on the train platform. Singularity continues to taunt Logan about how he knows him more than Logan knows himself, and how there isn't much difference from evil and good, hence looking into the Dark Mirror. After uttering his last words, Logan kicks Singularity right in the back, just as a speeding subway train heads towards him, killing him brutally and painfully as Logan reunites with Blake as well as Lian.
At base, Gabe learns from Lawrence Mujari and Teresa Lipan that Dark Mirror was a nerve gas that could kill millions by fusing with oxygen molecules. It grows more deadly as it spreads, and Singularity's single canister could have killed almost half of the population of Europe. It is the nerve gas equivalent to Syphon Filter: Both are the deadliest in their categories and are weapons of mass death.
Gabe goes to Addison's plaque at Arlington National Cemetery a week after the AIT assault and leaves a flower, the same flower Singularity used to genetically engineer the nerve gas Dark Mirror. After minutes of quiet reflection (credits begin to roll), he turns around to find none other than Addison, alive and well. 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.
He wants to tell Blake the newfound truth and is furious that Addison would hold such an important secret from him. She responds by mentioning that he will never want to leave the Agency, so he could end up causing indirect harm to Blake. She begs Gabe to let them leave in peace. He reluctantly agrees. Gabe is forced to watch his former love and his only child ride off into the sunset, broken-hearted and alone once again.
A bonus level in Bangkok reveals an alternate ending, taking place after the AIT assault, and Gabe's revelation. Jimmy Zhou, a gang leader tries to use 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 chain gun. Gabe kills them all, bursts in and shoots Zhou with the Desert Express .50. He testifies of his obsession with Lian as the copter arrives to extract them.
- Insertion Point Alpha
- Red Jack
- Finding Freeman
- A Man Without Power
- Freeman's Files
- Under NORAD's Nose
- Security Section D
- Kreisler's Garden
- Freeman's Answer
- Old Friends
- Forged Under Fire
- Traitor in Our Midst
- The Ultimate Sacrifice
- The Trojan Horse
- Fist Full of Rubles
- Blood Money
- Meeting with Fate
- Into the Abyss
- Red Section
- Event Horizon
- Matter's End
- Goodnight Sweetheart
- KemSynth Tower
- Sana Yemen
- Birds of a Feather
- Jimmy Zhou's Army