Some time after the events of Syphon Filter: Dark Mirror, Gabriel Logan receives an assignment from a "pencil neck" named Robert Cordell. A United States Naval supply ship, the U.S.S. Mt. St. Helens, has been boarded by Somali "pirates" in the Indian Ocean and is being led by a Syrian, Ghassan al-Bitar. Logan is supposed to secure the classified contents of Hold Five. Cordell explains to Logan that he is the only option because he cannot expect special operations to keep any secrets. Despite Teresa Lipan's protests, Gabe accepts the assignment to tie up loose ends with Bitar.
Upon arrival by helicopter, Gabe's pilot, Alima Haddad, tells Gabe that a distress signal coming from U.S. special operations has been broadcasting for hours. Gabe realizes that Cordell did indeed rely on Spec Forces, so the "pencil neck" was either keeping sensitive data from him, or lying to him. After fighting the pirates on deck, he learns from a dying special operations soldier that the squad's missions failed due to Cordell's incomplete intelligence. Gabe surmised that the attack was complex enough for Bitar's terrorist group, Al-Jamil, to be involved. Gabe fights his way to the cargo hold, with Alima Haddad being killed by an anti aircraft missile. Logan makes it to Hold Five, to find the cargo stolen. Gabe attempts to shoot down Bitar but misses. Cruise missiles were fired at the ship, with the missiles impacting before Teresa's warning was finished. Gabe kills Fahid, the commander of the piracy operation and escapes when a cruise missile hits the bridge. Upon returning to headquarters, Gabe finds out that Cordell accused Lian Xing of being a double agent, while presenting photos of her and a man in Cyprus.
Gabe enlists the help of an old friend Dane Bishop. They visit the wreckage of the St. Helens where they find Russian Spetsnaz are sweeping the area. Gabe helps Bishop move mines that the divers planted and protects Bishop's minisub. Dane cuts a hole in the hull, and Gabe is sucked into the wreckage.
Inside, he finds Surgeyev, a Russian henchman. With Bishop's help, he gains access to the nuclear warhead storage facility and blows open a heavy door. They meet up and fight their way into the reactor room, where they switch off the ship's systems, but then Surgeyev ambushes them. Gabe kills the enemy and heads back into the ocean with Bishop.
They swim around looking for Bishop's minisub, clearing out Russian divers as they go. They find Bishop's minisub, but it is partially damaged so Gabe acquires an item from the Agency helicopter and uses it to repair the minisub. A Spetsnaz submarine attempts to destroy Bishop's minisub, so he distracts the submarine while Gabe uses depth charges to disable the Russians. When the submarine is damaged, Gabe rips out the control valves to sink it. Upon completion of their mission, Gabe and Dane head home.
Gabe learns of the identity of the man in the photo, a Chinese scientist named Shen Rei, Lian's former husband. Shen was wanted by Cordell, the British and Chinese governments, as well as Bitar for a weaponized device called X-Z-2. Gabe also learns that Lian only went rogue to protect Shen. Logan travels to Azerbaijan to look for Maggie Powers, a British MI6 agent who will hopefully help him find Lian. There he finds that Russian Spetsnaz have been waging war with a resistance group. He also discovers a note from Maggie that she has been captured and wants him to leave. Ignoring her comments, Logan continues on and helps the resistance leader destroy an armoured convoy.
The resistance leader directs him to a hotel where Lian supposedly stayed. Gabe infiltrates the hotel and is almost killed. He holds the killer at gunpoint and finds out she is a Chinese agent. They fight the Spetsnaz together until Trinidad, the Chinese agent, tricks Gabe into giving her a boost onto the rooftops. She escapes and Gabe has to track her then provide covering fire for her. They make it to the rooftops where a large Spetsnaz group ambush them, and snipers try to take them out, but the duo eventually clear out all the patrols. Trinidad directs Gabe to jump off the roofs into a canal, and then disappears. Gabe continues searching for Maggie, and finds her inside the Spetsnaz command post. He kills the Russian thugs and then frees Maggie, but then a gunship attacks them. Maggie procures an RPG - 7 from the weapons stash inside the command post and uses it to destroy the helicopter. Gabe cannot find a missile launcher himself, so he directs Maggie to fire on the aircraft.
When they finally bring down the gunship, Kudrenko and two thugs confront them. They are taken to the Gebel Tyorma prison complex in the Republic of Georgia, where Trinidad approaches Gabe. She briefly tells Logan about how Lian and her were connected - she used to train Lian before she defected and her student's mistake caused her reputation to be blemished. Because of this, she enlists Gabe's help to assist her in finding Shen Rei, and loosens Logan's cuffs when he agrees to help. Seeing the Spetsnaz return, Trinidad hides herself and escapes in a stealthy method, leaving Gabe to fend for himself. He takes out the patrols and rescues Maggie Powers. They find a sewage disposal pipe inside the shower room and crawl into the outside of the base. There they fight their way through thugs and an armoured convoy, with Maggie covering Gabe when a sniper ambushed him. However, Gabe also learns that Cordell has shut down the Agency due to his inability to secure the contents of Hold Five.
They arrive inside an airfield and infiltrate a plane. Gabe helps Maggie who is flying the craft find a transponder, but halfway through his assignment he finds Spetsnaz patrols trying to break into the cockpit. He prevents the breach and moves on, but cannot find the transponder. Eventually he sees Kudrenko, who challenges him to a duel to the death. Logan kills Kudrenko and then a NATO escort directs Maggie to land the plane in a Syrian airstrip.
Cordell accosts Logan upon the plane landing, capturing Maggie and taking her into custody. He tells Logan to retire, saying that the business contains too many secrets. Gabe listens to him at first, but a note inside his apartment directs him to Tommy's Boxing Gym in downtown Langley, Virginia. While Trinidad watches him, Gabe goes into the gym and finds Teresa. She informs him that she set up a backup communications center in the gym since Cordell put the Agency out of commission. She also give Gabe the information he needs - Cordell is planning to bombard hidden caves in the desert, where Lian is held. Gabe goes to the desert and helps a tank commander who lost his allies to the enemies, who happen to be Bitar's thugs. Along the way to Bitar's bunker, Gabe finds evidence that Cordell ordered a squad of Desert Scorpions to jump into enemy territory, but due to his haste, the Scorpions parachuted in broad daylight, causing a massacre when anti aircraft artillery cut them down.
Gabe and the tank commander eventually arrive at a bridge, where they clear out the enemy patrols. As they make their way across the bridge, Gabe sees C4 explosives set on it. While he hurriedly has the tank back off, the bombs go off, sending Logan and the tank into the canyon below. Gabe somehow survives the ambush but the tank commander is presumably killed.
Logan wakes up to the sound of gunfire and kills the enemy patrols trying to eliminate him. He makes his way to a series of overhead ledges and helps a Special Op crew call in air strikes to destroy the turrets guarding Bitar's bunker. When the artillery is destroyed, the Special Op leads Gabe to a demolitions expert Boomer. They eliminate the enemy threat while Boomer sets up C4 at a door to let Gabe into the base. Both take cover, but Boomer seemingly dies.
Gabe finds incriminating evidence on Cordell wanting the weapon inside the base. He goes on to find Lian and rescues her. They escape from the base but find that Malak, another of Bitar's elites, is waiting to ambush them. They eliminate him using electronic weapons to disable his armour then they shoot him. When they return, Gabe hands the proof to Cordell and the latter is taken into custody.
Logan goes to Bitar's dam and Lian helps him provide a diversion. Gabe destroys the power substations and uses a keycard to access the spillway but Lian has disobeyed her orders. She goes in to find Shen while Gabe goes on with the mission. He destroys turbines to disable the dam further and eliminates troops equipped with antistatic armour.
He travels deeper into the dam complex and discovers evidence that Trinidad is inside the compound. He finds her inside the crane control room and threatens to shoot her, so she gives him an access code that will override the crane's security mechanisms allowing him to manually control it. After Logan enters the code, he unties her despite Teresa's warnings to leave her alone. She uses her chance to escape from Logan, but he is too busy to catch her. Instead, he operates the crane and destroys the door.
He heads to another wing of the compound and accesses the charge room. Bitar sees him and escapes with one device leaving Shen behind. Logan works with him and removes the X - Z - 2 devices from the machinery. Eventually they meet up with Lian while Gabe finds Bitar.
He sees Bitar on a cargo elevator and procures one such lift to chase the enemies. He shoots hydraulic tanks to slow down Bitar and finds him almost invulnerable due to his antistatic armour, so he shoots the X-Z-2 causing an explosion that kills Bitar.
Eventually, Shen commits suicide to avoid capture by the Chinese CSS agent, Trinidad. Gabe considers retiring after the ordeal due to the nature of their work, only for fellow IPCA agent Lawrence Mujari to be killed and Teresa to be wounded by Trinidad, while an injured Gabe kills her in turn. Lian gives Gabe CPR, leaving the fates of Gabe and Teresa unknown.
- Pirates of Somalia
- Going Under
- Ocean's Five
- Sea of Darkness
- What Lies Below
- Depths of Darkness
- Dead Currents
- Missing Friends
- Found Enemies
- Nowhere to Run
- Into the Cold
- Deadly Cargo
- Operation Canyon Storm
- Our Hidden Past
- Desert Flames
- The Long Descent
- Leading the Blind
- With Violent Intent
- Killing Time
- Lian's First Time
- Behind the Scenes
- Left Behind
As with Dark Mirror, Logan's Shadow is a third person shooter game that includes elements of stealth and firepower. Underwater levels, which have never been seen before, make an appearance with special weapons (such as harpoon rifles, bolt cannons and other firearms), puzzles and 3D movement. Blind fire makes an appearance which allows the player to shoot from cover that forces the enemies to run to cover.