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1* AlternativeCharacterInterpretation: 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 SuspiciouslySpecificDenial, 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 NotWorthKilling 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?
2* AmericansHateTingle: While many consider ''3'' as a SophomoreSlump 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.
3* AntiClimaxBoss:
4** 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.
5** 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.
6** 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.
7* AssPull: [[spoiler:Chance]] being a traitor makes no sense since he as Unit One has a different voice actor.
8* SugarWiki/AwesomeMusic:
9** ''Syphon Filter'':
10*** [[https://www.youtube.com/watch?v=LIKQKlUWIPA The iconic title screen theme of the PlayStation trilogy]]; sounds catchy, suitable to set the players in the mood before the game starts.
11*** [[https://www.youtube.com/watch?v=K-l9SC7HICA "Freedom Memorial", a.k.a. Anton Girdeux boss fight music]] and its remix version [[https://www.youtube.com/watch?v=GjCu-ATjuOI&t=122s "Base Tower", which is played in a battle against enemy chopper]]. Opinions about which one is better may vary, but there is no doubt that both music are amazing, especially knowing the fact that this is the first action shooting game for the developer.
12*** [[https://www.youtube.com/watch?v=ObHVmo96jXQ&t=30s "Expo Center Reception"]], which also plays in the second game fits the espionage theme well.
13** ''Syphon Filter 2'':
14*** [[https://www.youtube.com/watch?v=CF61E_JgdHk&t=2s "United Pacific Train 101"]] is an adrenaline-pumping music, which is suitable for Gabe's never give up attitude and the gunfights that happen on runaway trains.
15*** [[https://www.youtube.com/watch?v=S0tvc9IG9zQ "Club 32" proves that dubsteps can sound heavy]].
16*** The intense [[https://www.youtube.com/watch?v=ujxNNPQQsU8 boss fight]] music from ''Syphon Filter 2'', specially on the boss fight against [[spoiler:Jason Chance]].
17*** [[https://www.youtube.com/watch?v=V7bmLGKPLDo This music plays in "Agency Bio Lab Escape" and "Aljir Prison Escape" (danger)]]. Combination of fast paced techno music with the alarm sounds and gunshots as the base goes alert makes this game memorable.
18** ''Syphon Filter 3'':
19*** [[https://www.youtube.com/watch?v=RIllX2jpR8c "Paradise Ridge"]] and [[https://www.youtube.com/watch?v=DDG0545zsxU&t=27s its alert counterpart]] are played in the Montana levels. The suspenseful element manages to make the player realizing how dire the situation is, between rescuing teammates, avoiding gunfights with angry townsfolks and fending off corrupt agents.
20* BrokenBase: 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.
21* CompleteMonster: [[PlayerCharacter Gabe]] and [[TheLancer Lian]] have faced many terrible people in their mission to stop the titular [[ThePlague virus]], with these being the worst:
22** [[CorruptPolitician Vincent Hadden]], the BigBad 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 [[ArmsDealer 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.
23** First and third games: [[TerroristWithoutACause 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 [[WorldWarIII a third World War]].
24** ''The Omega Strain'': [[CorruptCorporateExecutive Mihai Niculescu]] is the GreaterScopeVillain of the original trilogy, and [[BigBadEnsemble 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 [[WarForFunAndProfit 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 [[PoisonAndCureGambit sell a vaccine]] to the survivors.
25* FriendlyFandoms: With ''VideoGame/{{Tenchu}}'', due to the similar suspenseful atmosphere and the camaraderie between Rikimaru & Ayame and Gabe & Lian.
26* GameBreaker:
27** 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.
28** The Spyder Skorpion sub-machine gun in ''Syphon Filter 3''. Ridiculously overpowered, this weapon can shred through enemies in split-seconds.
29** 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.
30** 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.
31** Possessing [[StuffBlowingUp explosive weapons such as the M-79, MIL-15, and Grenades]] as well as SniperRifle in [[PlayerVersusPlayer 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.
32* GoodBadBugs:
33** 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.
34** In the last stage of ''3'', [[spoiler: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 [[spoiler:Mara]] and slowly backs away until the bulletproof glass panel poofs out of existence, a simple pistol can do the job.
35** 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.
36* HarsherInHindsight:
37** 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''.
38** 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.
39* ItsTheSameNowItSucks: A common complaint is that the original trilogy's barely changed over time, in both graphics and gameplay.
40* LesYay: Gary Stoneman confirms [[spoiler: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).
41* LowTierLetdown: Ellis is often bashed by many fans due to his mediocre combat skills in ''3''[='=]s Convoy level, making him TheLoad most of the time.
42* MemeticMutation:
43** 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 [[BringMyBrownPants didn't have enough time to get to the bathroom]].
44** 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:
45-->''' OK. I live in Uzhhorod, and I don't remember this shit.'''\
46'''Lol, I live in Rozovka, it's just a village.'''
47* SugarWiki/MostWonderfulSound: Mara's laugh in the first game is this for some.
48* {{Narm}}:
49** 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.
50** Gabe is supposed to be a OneManArmy 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 ScreamsLikeALittleGirl when he gets set on fire or takes a big fall in the plot.
51* NarmCharm: For some, the voice acting in the original trilogy veers back into this.
52* RescuedFromTheScrappyHeap: 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]]when Gabe takes too long fighting mooks[[/note]], "Where are you going?"[[note]]when Gabe picks up flak jackets and ammo left behind by the mooks he or Lian killed[[/note]], and "Are you crazy!?"[[note]]when Gabe shoots Lian in a friendly fire, even if it's accidental[[/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.
53* RetroactiveRecognition: Rhoemer has the future voice of both [[VideoGame/SamAndMax Specs]] and [[VideoGame/BioShock2 Augustus Sinclair]].
54* TheScrappy: Imani thinks she is [[Series/TwentyFour Jack Bauer]] but ends up being a lot bitchier, constantly harassing and putting down the player, [[spoiler: only to end up killed early in the game.]]
55* TheScrappy: Ellis is often bashed by many fans due to his mediocre combat skills in ''3''[='=]s Convoy level, making him TheLoad 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.
56* ScrappyMechanic:
57** 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.
58** 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.
59* SpecialEffectsFailure: 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, [[LawOfConservationOfDetail saving the developers some trouble]].
60* SuspiciouslySimilarSong: The song playing ''2''[='=]s Club 32 sounds like a techno version of [[Music/{{ABBA}} "Dancing Queen"]].
61* ThatOneLevel:
62** ''Syphon Filter'':
63*** In the Washington Park level, you have to make precise silenced-night vision sniper shots at the tennis courts.
64*** The Expo Center Reception level relies on evading or shooting multiple mooks.
65*** 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.
66*** The Base Tower level requires you to have enough ammo to fend off a helicopter whose pilot shoots automatic rounds at you.
67*** The Rhoemer’s Stronghold, Stronghold Lower Level, and Stronghold Catacombs levels are sprawling. Fun to play, but extremely open world for its time.
68*** 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.
69*** The Missile Silo level requires you to navigate a series of catwalks and metal beams to disarm the missile ''and'' escape before it launches.
70** ''Syphon Filter 2'':
71*** 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.
72*** 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.
73*** The New York Sewers level features narrow passages, almost no cover, and infinitely [[RespawningEnemies respawning]] Agency EliteMooks randomly appearing both in front and behind you.
74** ''Syphon Filter 3'':
75*** 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.
76** ''The Omega Strain'':
77*** 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]]Technically, you can still continue the game if you're spotted in Gabe's mission, but it's next to impossible to beat in the time limit you're given.[[/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.
78* TheyWastedAPerfectlyGoodCharacter: 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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