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  • Alternative Character Interpretation: In 2, Lian encounters Mara in Russia while both are looking for Gregorov; Mara has her chauffeur driving her in a limousine while Lian is on foot. Mara has the chance to kill Lian there, but decides to just let her be and tells her driver to drive forward. There is also another cutscene that shows Mara telling her boss that she doesn't see Gabriel Logan, which counts as a Suspiciously Specific Denial, as she mentions Gabe's name to prevent herself from having to mention seeing Lian in Russia. Why does Mara do that? Does she feel sorry for Lian due to being infected with a deadly virus? Does she think of Lian as a weak Not Worth Killing frail? Or does she think that Lian is more useful to her as a bargaining chip to deal with Gabe Logan by leaving her alive but ill?
  • Americans Hate Tingle: While many consider 3 as a Sophomore Slump of the series, this particular installment is infamously disliked in Ireland and Northern Ireland because two Dublin levels portray IRA as enemies and MI-6 as allies of justice that help the protagonist stopping terrorism. Even with the publisher releasing EU version that changed IRA into ARM, this installment's popularity did not improve that much.
  • Anti-Climax Boss:
    • You're up against Rhoemer at the final level of the original Syphon Filter and he's armed with an M-79, which can kill you in one hit. There are two details that make what should've been a epic gunfight into a let-down: First, Rhoemer is standing in defilade between the mainframes with no line of fire unless you give it to him. And second, the game is scripted to have Rhoemer die from a Gas Grenade, meaning that he goes out with a whimper instead of a bang.
    • Dillon Morgan, once Teresa defuses all his bombs in China Exhibit, is surprisingly easy to beat if Gabe still has ammo for crossbow from the previous level, as crossbow has high accuracy and arrows are designed to penetrate bulletproof armors. If the player locks on Morgan with auto-aim and has Gabe shot him with crossbow before the latter shoots his M-79 grenade launcher, the fight is as good as done.
    • Shi Hao is the most ambitious Syphon Filter potential buyer, who goes rogue and leads his army rebelling against PRC and Russia, yet he is easily defeated and killed by Gabe, as he wields normal gun with mediocre accuracy, and he does not even wear bulletproof vest.
  • Ass Pull: Chance being a traitor makes no sense since he as Unit One has a different voice actor.
  • Awesome Music:
  • Broken Base: The changes of gameplay between the PS1 trilogy and the PSP/PS2 continuity. One half of the fandom criticize the PS1 trilogy for keeping the stagnant gameplay and welcome the significant changes in the newer games, the other half dislike the changes in newer games such as the absence of combat roll in Dark Mirror, 'unnecessary' romantic sub plots and that they just prefer the PS1 trilogy.
  • Complete Monster: Gabe and Lian have faced many terrible people in their mission to stop the titular virus, with these being the worst:
    • Vincent Hadden, the Big Bad of the original trilogy, is the traitorous Secretary of State and head of the Agency who seeks to increase his political power. Working for the corrupt Mihai Niculescu, Hadden secretly creates the Arms Consortium, an illegal black market where weapons would be sold to foreign terrorists, planning to sell the Siphon Filter virus at a high price. He plans to have terrorists use the virus to wreak havoc on American soil and step in to save the day, hoping to use that clout to become President. Selling the virus to rebellious Chinese General Shi-Hao, knowing full well that he would use it to infect China and Russia and start a war with them, he kills any of his agents aware of the conspiracy. When Gabe starts getting in the way of his plans, Hadden tries to have him and Lian arrested and blamed for the conspiracy, hoping to throw everyone working for him under the bus and escape scot-free.
    • First and third games: Erich Rhoemer is the leader of the terrorist organization Black Baton, and Gabe's most personal enemy. Responsible for multiple bombings and plane hijackings before partnering with Pharcom, Rhoemer is placed in charge of creating the Syphon Filter virus. Hearing that the Agency sent men out to stop him, he captures, tortures, and holds Agent Ellis captive, then has his laboratory burned, the cure destroyed, and Ellis executed once Gabe and Lian arrive. Escaping to Washington, D.C., he detonates the city's subway system and has multiple virus-filled bombs planted in a park in an attempt to infect the entire city. When Gabe invades his hideout, Rhoemer kidnaps and infects Lian with the virus. Occupying underground catacombs, he has people captured and used as test subjects for the virus, ordering every one of them executed when Gabe is caught sneaking around. Rhoemer later decides to steal a nuclear missile, fill it with the virus, and launch it anywhere, not caring where it lands or the possibility that it might start a third World War.
    • The Omega Strain: Mihai Niculescu is the Greater-Scope Villain of the original trilogy, and one of the game's main threats. A psychotic banker, Mihai created the Syphon Filter virus as a bioweapon to be sold for money, using his connections to have it sold to countless terrorist and criminal groups, which he also funds with his own bank money. Using Vincent Hadden's Consortium as a way to sell the virus, Niculescu allowed Hadden to kill anybody who came close to the conspiracy and start wars to keep the virus profitable, having Mara Aramov murder him when his plans are exposed. Creating the Omega Strain virus to be more powerful than his previous Syphon Filter, Niculescu allows the rogue Ivankov to nuke Moscow, believing the missile to be filled with his own virus, and hoping to sell a vaccine to the survivors.
  • Friendly Fandoms: With Tenchu, due to the similar suspenseful atmosphere and the camaraderie between Rikimaru & Ayame and Gabe & Lian.
  • Game-Breaker:
    • The air taser. It has infinite range, infinite ammo, is considered to be a stealth weapon, and can kill a helluva lot of baddies in relatively short time. Plus it's fun to hear them scream and see them catch on fire.
    • The Spyder Skorpion sub-machine gun in Syphon Filter 3. Ridiculously overpowered, this weapon can shred through enemies in split-seconds.
    • The K364 in the original trilogy. It's an assault rifle that pierces through flak jackets, killing armored enemies without the need for a precision headshot.
    • In The Omega Strain, the E.P.D.D., an advanced version of the air taser, is the best weapon in the game, as it has ridiculous range, and can sometimes punch through flak jackets (usually in two hits), meaning that you can kill almost anyone you come across.
    • Possessing explosive weapons such as the M-79, MIL-15, and Grenades as well as Sniper Rifle in two players mode will make it clear which player acts as the predator and which player acts as the prey. Granted, when someone dies, they drop all their weapons (which can be collected) and respawn at random place with only a handgun and a knife.
  • Good Bad Bugs:
    • In "Base Escape" level from 1, if Gabe shoots at one of virus-filled missiles accross the level, Lian will give him a stern warning through the radio communication, even though she is supposed to be killed or kidnapped by Rhoemer in the previous level, hence unable to give any briefing to Gabe.
    • In the last stage of 3, Mara Aramov is hiding behind bulletproof glass with a hostage whom she'll kill if one gets too close. Normally, you'll need the gun that shoots through walls, get above her and snipe her through the floor. However, due to hardware limitations, the environment tends to get flushed out after a certain distance to save memory. This means that, if one keeps targeting Mara and slowly backs away until the bulletproof glass panel poofs out of existence, a simple pistol can do the job.
    • In The Omega Strain, enemies will sometimes appear with weapons stuck in their necks, making it impossible to shoot the player, who can run around without fear of being hit. However, it can happen to the player as well.
  • Harsher in Hindsight:
    • In 2, about halfway into the game, Lian arranges a meeting with a former partner, Gregorov, at a neutral meeting point: a techno dance club. But their meet-up is ruined by an attack on the club in an attempt to assassinate Lian. And the date that this happens on in the mission dossier? 09/11.
    • In 3, the first mission takes place in a Tokyo hotel called the "Fukushima Hotel". Surely a name chosen completely at random at the time, but carries a much darker association in the years since.
  • It's the Same, Now It Sucks!: A common complaint is that the original trilogy's barely changed over time, in both graphics and gameplay.
  • Les Yay: Gary Stoneman confirms Mara Aramov and Elsa Weissinger are in a canon relationship by using his rifle scope in the Dark Mirror bonus mission (only in hard mode).
  • Low-Tier Letdown: Ellis is often bashed by many fans due to his mediocre combat skills in 3's Convoy level, making him The Load most of the time.
  • Memetic Mutation:
    • Gabe's running animation in the first three games, due to how goofy it looks. Many like to think that he runs like that because he didn't have enough time to get to the bathroom.
    • Some missions in the PS1 trilogy feature super-secret military base with advanced technology hidden in a rather ordinary, if not remote village in real life. This detail did not escape fans who actually lived in said area:
    OK. I live in Uzhhorod, and I don't remember this shit.
    Lol, I live in Rozovka, it's just a village.
  • Most Wonderful Sound: Mara's laugh in the first game is this for some.
  • Narm:
    • The voice acting for the original trilogy could be rough, with fake stereotypical accents all over the place, and it meshed hilariously with motion captured character models that often looked more like walking tall LEGO people rather than human beings. Especially if it cuts in up close where they suddenly gain an awkwardly-animated 2D face texture.
    • Gabe is supposed to be a One-Man Army super agent badass that the story loves to hype up as being unstoppable. He also runs like he shat himself, stumbles from every fall like he has no idea what he's doing while flailing around, and Screams Like a Little Girl when he gets set on fire or takes a big fall in the plot.
  • Narm Charm: For some, the voice acting in the original trilogy veers back into this.
  • Rescued from the Scrappy Heap: There was a significant part of the fanbase who found Lian annoying when the first game came out. Her chastising tone in the Stronghold Catacomb level when Gabe needs to escort her has her saying things like "What are you doing?"note , "Where are you going?"note , and "Are you crazy!?"note  made the already difficult level becoming more frustrating. It took the sequel in which she has less chastising tone, combined with her being playable in the story mode and the sympathy factor where she can do her tasks flawlessly despite being ill, for Lian to earn the fans' favor.
  • Retroactive Recognition: Rhoemer has the future voice of both Specs and Augustus Sinclair.
  • The Scrappy: Imani thinks she is Jack Bauer but ends up being a lot bitchier, constantly harassing and putting down the player, only to end up killed early in the game.
  • The Scrappy: Ellis is often bashed by many fans due to his mediocre combat skills in 3's Convoy level, making him The Load most of the time. Because of this, some people don't feel bad when he died in Gabe's Costa Rica level which was based on first game's prologue.
  • Scrappy Mechanic:
    • The flashlight in the first game. To use it you had to unequip your weapons, as only one item could be equipped at the same time. Not only that, but the light would alert any mooks nearby, making it actively dangerous to navigate through dark areas with it equipped, while alternatives such as the Nightvision Rifle and the Viral Scanner (both of which allowed the player to see dark areas in front without alerting enemies, albeit with much less detail) were just slight improvements. Starting with the second game the player got nightvision goggles instead, equipped automatically in any area that required them, making dark areas much less of a hassle.
    • If the next mission immediately picks up where the last one left off in the PS1 trilogy, all of your gear remains intact — which also means your ammo and health/armor do too. It's entirely plausible to clear one level, especially the nasty boss fights, and then get thrown into the next one where it's almost to outright Unwinnable without a total mission reset.
  • Special Effects Failure: The intro cutscene of the PHARCOM Warehouses level has flashing lights happening around the map to simulate battles being fought between Phagan's men and Rhoemer's men. But they forgot to put the character models in, making the entire cutscene look like the warehouses are being attacked by ghosts. Granted, the idea might be that they're too small to see from the height Gabe and co. are flying, saving the developers some trouble.
  • Suspiciously Similar Song: The song playing 2's Club 32 sounds like a techno version of "Dancing Queen".
  • That One Level:
    • Syphon Filter:
      • In the Washington Park level, you have to make precise silenced-night vision sniper shots at the tennis courts.
      • The Expo Center Reception level relies on evading or shooting multiple mooks.
      • In the Rhoemer’s Base level, Gabe has to plant C4 on each of the base's fuel tanks and disable the laser censor leading to the bunker while remaining unseen by the mooks. While stealth is not mandatory, getting spotted will result in some mooks alerting the base, and soon infinitely respawning mooks will actively chase Gabe for the rest of the level. What makes open gunfighting unfavorable is that all respawning mooks surround Gabe with heavy weapons such as Combat Shotgun or PK-102 which wear down his armor in short time, and the only armor available in this level is the one wielded by Gabrek (which can be taken from his dead body given Gabe killed him with a head shot or by using a Gas Grenade). Other than that, Gabe has to survive the whole base's onslaught until he enters the bunker, and fortunately there is a crate containing an armor near the bunker's starting point.
      • The Base Tower level requires you to have enough ammo to fend off a helicopter whose pilot shoots automatic rounds at you.
      • The Rhoemer’s Stronghold, Stronghold Lower Level, and Stronghold Catacombs levels are sprawling. Fun to play, but extremely open world for its time.
      • The PHARCOM Warehouses level has infinite spawning mooks and a very confusing layout. Also, you have to use the infrared-style device to get what you need to advance, which are not at all easy to find, and you are not at all told that you needed to use them.
      • The Missile Silo level requires you to navigate a series of catwalks and metal beams to disarm the missile and escape before it launches.
    • Syphon Filter 2:
      • I-70 Mountain Bridge level requires you to assassinate the enemy commander and disable all of the bombs scattered under the bridge while remain stealthy for first half of the level. At the beginning of the level, you don't have any silenced weapons other than a knife and you need to obtain more silenced weapons to kill your way to the tunnel undetected.
      • Agency Bio-Lab level is a complicated stealth mission in a maze-like terrain, where you have to spend half of the level navigating the place without a map while avoiding guards and CCTV cameras altogether to find weapons and reach the lab's computer room in order to give Teresa necessary files.
      • The New York Sewers level features narrow passages, almost no cover, and infinitely respawning Agency Elite Mooks randomly appearing both in front and behind you.
    • Syphon Filter 3:
      • The Convoy level features almost no cover and you have to protect both your teammate Ellis and the already damaged truck from rebel gunmen, grenadiers, and snipers. The enemy guards are already aware of your presence, making stealth nonexistent and forcing you to confront enemies head on. It's regarded by fans as one of the hardest levels in the original trilogy.
    • The Omega Strain:
      • The bonus missions have you playing characters from the earlier games (Gabriel "Gabe" Logan, Teresa Lipan, Lawrence Mujari, etc.). Sounds cool, right? The problem is that these bonus missions can be quite long, have multiple objectives, are all stealth based, and if you get spotted, it's an instant game over. And because there are no checkpoints, if you fail, you have to start all over again from the beginning.note  This is especially problematic in Mujari's mission, where you have to sneak through a bombed-out village that has plenty of places for enemy soldiers to hide, and you can't kill any of them. The general consensus among Syphon Filter fans is that this is the most frustrating mission in the entire series.
  • They Wasted a Perfectly Good Character: Maggie Powers, an MI6 agent, is not playable in any game she appears in, despite being one of the most important supporting characters in the series.

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