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Griffith's Apostle army in Berserk, which also double as Mook Lieutenants.
Hotel Moscow in Black Lagoon has the Desantniki (who are called the "Vysotoniki" by Dutch), Balalaika's personal bodyguard and inner circle made up of former USSR paratroopers who fought under her in Afghanistan.
The Espada all tend to have a few lesser Arrancar that they keep around to serve this purpose, called their Fraccion. And frankly, the Big Bad considers all Arrancar to be this, at best. In the end, he considers them to be plain old Mooks after almost everyone but Harribel dies without killing a single shinigami.
Harribel's Fraccion fit this trope best of all. Why? They're by FAR the most effective of ANY Fraccion shown. While most of the Fraccion are defeated by, at best, the Number Twos of the various Gotei divisions, Harribel's trio manages to take out a grand total of FOUR Lieutenants (Matsumoto, Hinamori, Shuuhei, and Iba—in that order, and Kira was next) by summoning their pet Giant Mook. It took the Commander Generalhimself to get fed up and take them out.
The Stern Ritter are the elite fighting force of the Vandenreich, and their effectiveness against the rank-and-file Shinigami is shown in spades in the first invasion, and prominently in the second invasion. As it stands, the only true defeats inflicted upon the Stern Ritter have been by Zaraki, who is one of the Special War Potentials, Yamamoto, and Renji, Rukia and Byakuya after their Royal Guard training. While Kyoraku and Ukitake have yet to get into a serious fight, the rest of the Captains - barring Mayuri - have either been steam-rolled or won pyrrhic victories. The strongest of them could drop a meteor on the Seireitei, and these are just Yhwach's mooks.
Akuma of D.Gray-Man have levels, so that every time the exorcists get strong enough to Red Shirt-ify the current strongest akuma, they can just introduce a new strongest type.
Guyver gives us several. Compared to the average Chronos foot soldiers, the Chronos aligned Zoanoids could count as this trope as they are usually much more than a match for any normal human task force. In terms of the enemies the Guyvers themselves fight, Zoanoids usually become the normal Mooks while the Hyper-Zoanoids take on as members of this trope
Fairy Tail has Yomazu and Kowazu. The dark guild, Grimoire Heart, is lead by Hades with seven established lesser bosses who oversee the many Mook soldiers associated with Grimoire Heart. Yomazu and Kowazu however, are in between. They're strong enough to be classified higher then a Mook, even having established names, but not strong enough to be standing alongside the leaders. They beat up Gajeel and Levy before they are defeated by them. However, Gajeel is so injured, he's Put on a Bus until Hades' defeat.
Near the end of the "Enies Lobby" arc, Captain level Marines attack the Straw Hats at the Bridge of Hesitation. The Straw Hats has spent the rest of the arc taking out several thousand standard Mooks, as well as fighting the government's resident assassin team, CP9, so these Elite Mooks did pretty well against the worn out Straw Hats. Still got their butts handed to them, though. One of them scored a victory for mooks everywhere when he actually managed to destroy one of Zoro's swords. Usopp ended up sniping him down, but his actions left Zoro unable to use his strongest techniques for most of the next arc.
The Sorting Algorithm of Evil is justly used here, as well. The more and more "dangerous" the Straw Hats become, the more and more stronger marines they're gonna send out. When before, fighting a captain or commander could be the Big Bad of an arc, they're now just Elite Mooks for Luffy and the crew... except Smoker, who's more of a Boss in Mook Clothing. Throughout his time as a captain and a commodore, he's still handing Luffy his butt solely from the benefits of his Logiapowers.
The giant mecha in the festival arc of Mahou Sensei Negima! had their weaponry quietly upgraded to no longer fire mere stripper rays. Apart from that they were indistuinguishable from their predecessors.
An odd example occurs in the movie. While the majority of the combats in the series make it look like a big boss rush, the final battle in the movie is against a group of identical mooks that even carry "Mass Production" in their names.
On the ground there's the JSSDF, Keel Lorenz's shock troopers, sent to *ahem* "clean up" NERV once Keel's plans start going awry.
The red armoured Rublum forces of the Empire in Tears to Tiara. They hand the protagonists their first real defeat in episode 8, though that was due in part to Arthur's lack of strategy beyond "charge them and hope for the best". Well, they used logs too, but the Rublum soldiers just got back up after being hit by the logs.
In Vinland Saga, the viking kings call upon the Jomsvikings, a mercenary band for hire made up of war veterans, for elite muscle. Outside of fighting named characters with Character Shields, they're pretty much unstoppable.
The original Power Broker's business involved selling super-strength upgrades, often to villains looking to assemble Elite Mook units. The Broker himself employed a squad of such called the Sweat Shop.
Another Marvel subversive group, Advanced Idea Mechanics, started as the Elite Mooks of HYDRA (aka THEM), being its super-science division; AIM itself mass-produced synthetic soldiers like its "chemical androids" and Adaptoids. HYDRA itself developed robotic soldiers called Dreadnoughts for this purpose, and in some continuities HYDRA itself started out as or becomes the Elite Mook organization working for the Red Skull.
For more conventional criminals like Spider-Man and Daredevil archfoe the Kingpin of Crime, the Hand frequently serves as a group of killers and enforcers a cut above the average mob wiseguy. The Hand usually has its own plans, though. Unsurprisingly, the Hand and HYDRA share a history and have alternately served as elite mooks for one another on separate occasions.
The slavers. Not only did they use squad tactics and didn't panic during the first few seconds of The Punisher's attack, they even forced him to retreat. And they held their guns right.
Later, a group of generals sends a special forces squad after Frank precisely because they're the Army's elite.
Manute from Sin City had a squad of mobsters under his command but he sent a group of former IRA mercs to fight Dwight and the Old Town girls. They did a good job of it due to a lot of firepower and one managed to briefly catch Miho off-guard but they were all eventually defeated.
Though the original was introduced as an individual case of A.I. Is a Crapshoot and eventually transformed into the recurring villain Bastion, later X-Men stories have made the Nimrod type of Sentinels this in relation to the usual versions.
Transformers Monstrosity: Establishes the Terrorcons as one of the more powerful Decepticon fighting forces, able to take on Megatron, albeit weakened. In Transformers Windblade three of them go against Windblade's posse and come out victorious, Rippersnapper takes down Slug (a veteran Dinobot, which was one of the most powerful Autobot groups), Sinnertwin takes down both Blurr (another Autobot veteran) and Waspinator, and Cuthroat keeps Tankor (veteran Decepticon) and Windblade (above average fencer) on their toes, even with an impaled wing he's still fighting.
The SAS in ARSENAL are called in by SEELE to help Nightshift Bunnies Aoi Mogami, Kaede Agano, and Satsuki Ooi do battle with a Shinji Ikari-controlled NERV. They are slaughtered wholesale by Misato Katsuragi, Touji Suzuhara's younger sister, and Pen-Pen.
My Little Denarians: After battling through various less capable mooks, including Discorded Royal Guards and Stormtroopers, Harry and co. end up fighting the Denarian cultists, who ambush and flank, deploy from armoured vehicles, use grenades, heavy weapons and snipers, and generally act like a competent, well-trained paramilitary force. Harry thinks they're almost too competent to be willingly working for the Denarians.
In the Tamers Forever Series, Armaggedemon, Diaboramon, Infermon, LadyDevimon and SkullSatamon all serve this role in Daemon's army.
The Rise Of Darth Vulcan: Vulcan eventually gains a second group of minions in the form of the Crimson Guard, a group of Changelings recruited from Chrysalis, who are far more powerful (and competent) than his standard Diamond Dog soldiers.
The Assault Troopers from The TSAB – Acturus War, who are both mages and conventionally-trained special forces. We see only four named ones on-screen, but they do fairly well considering they end up fighting Nanoha, Fate, Vita and Signum.
Films — Live-Action
Near the end of Batman Begins, Ra's Al Ghul sends 4 serious-looking ninjas in full metal body armor to fight Batman. They do marginally better than everyone else who's tried to fight Batman up to this point until they pushed him into a mob.
Both Equilibrium and Ultraviolet feature the hero battling a group of several unique-looking Mooks armed with katanas, just before the final fight with the Big Bad. These guys are either Elite Mooks, or complete idiots, for fighting only with swords in a world where everyone is equipped with automatic weapons. In any case they don't do noticeably better against the hero than all the previous Mooks...i.e. they all get killed in about 6 or 7 seconds.
In The Expendables, there is General Garza's special forces, identified by their red berets, jungle camouflage, and green-and-yellow facepaint. They actually live up to their reputation as well, forcing the Expendables to seriously work to kill them, unlike the regular soldiers who they mow down with regularity.
Averted in John Woo's Heroes Shed No Tears. The so-called Black Squadron are the personal guard of the general responsible for the region's drug trade and are all dressed in black instead of regular military uniforms. However, they're the first mooks fought and are actually less competent than the regular Vietnamese soldiers, who put up slightly more of a fight before going down.
In Inception, this is the difference between an untrained mind's projections and a trained one. Normally, a mind's subconscious projections take on the form of waves of mindless civilians that swarm intruders in the dreamworlds, while if a mind has been trained to resist intrusion, the projections are armed with heavy weaponry and attack in coordinated groups.
The Uruk-Hai in The Lord of the Rings movies, though after their introduction they don't seem to pose much of a problem.
In The Matrix Reloaded, this is the excuse for Neo still having to get into martial arts battles with the Agents, despite apparently transcending hand-to-hand combat at the end of the first film. After an exchange with the new agents, we says, "Hmm, upgrades!" The agents don't actually seem to be any tougher than the previous set in comparison to anyone else.
Agents of the East India Co. in Pirates of the Caribbean: Dead Man's Chest. We only see one of them (Mercer) but Jack "vanished from under the eyes of seven agents of the East India Company" and this is listed as an impressive feat.
The Super Battle Droids and destroyer droids (droidekas) in Star Wars: Attack of the Clones.
General Grievous' Magna Guards, non-Jedi droids who are able to fight against Jedi in melee combat and do relatively well (i.e. live longer than about 6 or 7 seconds).
The Royal Guard, the guys in red, are supposed to look like elite mooks, at least. They don't do anything in the original series and get curb stomped by Yoda in the prequels.
The Expanded Universe gives us Darth Vader's 501st Legion (named after the fan club), stormtroopers who can actually shoot straight. Justified because canonically, the Legion remains composed purely of clone troops and not ordinary recruits.
The Expanded Universe also asserts that the Stormtrooper Corps are also the Elite Mooks of the Empire; the Imperial Army (which the Corps are not a part of) is actually the mook component, though the movies would have you believe otherwise.
300 applied Action Movie tropes to historical events, including making the Persian 10,000 Immortals Elite Mooks.
The Cardinal's Guard in the 1973-4 film versions of The Three Musketeers probably qualify. Although the novel depicts them as more or less equal to the king's musketeers in training and prestige—and in the first fight sequence the musketeers hesitate before taking them on at 1-2 odds—by the final fight sequences, the heroes are dispatching them by the dozen.
The Black Demon Ninjas from Violent Shit III: Infantry of Doom.
The Einsatzkommando from the movie adaptation of The Keep. Just as in the novel, however, they're "elite" in name only, and are no more effective against Molasar than their regular German army counterparts. In fact, as Woermann points out, the only thing these "elite" troops do effectively is slaughter large numbers of unarmed civilians (which in real life was the Einsatzkommando's entire reason for existing — they were mobile death squads).
In Lone Wolf, the Giaks are the lowly mooks of the Darklords, while the Drakkarim, black-armored warriors wearing death masks, are the elite. Further in the series, the ante is upped with the elite of Drakkarim, the Death Knights.
In Cerberon Wizard Royal Elect Tmneal Kravat has a group of half-hackal warriors called the Nine Fangs explicitly described as elite soldiers. Their eliteness seems more like an Informed Ability when Aladavan fries them with a massive ball of lightning, and decapitates the blinded and severely burned survivors who are still trying to achieve their objective despite their fatal injuries.
The ur-viles from the Chronicles of Thomas Covenant are an interesting example. They're no stronger than the stock mooks, Cavewights (who are physically powerful but weak-willed), but are far more dangerous because they're smarter (Cavewights will just Zerg Rush the enemy; ur-viles always fight in disciplined formations) and possess potent magic (ur-vile loremasters, their primary magic-users, can cause even experienced warriors to freak when they show up).
Source material notwithstanding, the Warhammer 40,000: Gaunts Ghosts novels after Necropolis had them fighting the Blood Pact, the retinue of the Chaos warlord they were fighting against, who were supposedly better than the generic heretics and zealots that came before. The Guns of Tanith also introduced Loxatl mercenaries that could take lots of lasfire.
The Steel Inquisitors. A little more elite than most Elite Mooks, in the first book only Sazed and Kelsier can take them on and live, and it's still not very advisable. Kelsier killing one is treated like him snatching the sun out of the sky: everybody around falls still and can't believe their eyes. Oh, and they have literal Spikes of Villainy...through both of their eyes.
Hazekillers (who are warriors specially trained to kill allomancers), and koloss are Elite Mooks who are more powerful than regular Mooks, but less powerful than Inquisitors.
Arawn employs two main varieties in the Prydain Chronicles, each with their own particular twist. The Cauldron-Born are undead, implacable, and virtually impervious to injury, but they're also progressively weakened the further they get from Annuvin, making them more useful as elite guards than as an assault force. The Huntsmen of Annuvin, in contrast, are mortal men, but are magically bound to have Undying Loyalty to Arawn and also have the Conservation of Ninjutsu as a superpower, with every surviving Huntsman becoming stronger whenever one is killed. They're more often used as fast moving strike forces and skirmishers.
The Wheel of Time has the Myrddraal, also known as the Eyeless. They use spirit vision of a sort to transcend being physically blind and their melee skills are implied to be in part due to being "out of sync with time".
The Keep has the SS Einsatzkommando, led by Major Kaempffer, sent in after the regular German soldiers keep falling to an unseen menace. They're a subversion, though. Although they have better weaponry, more authority due to being SS, and flashier uniforms, in practice they fare no better against Rasalom than the regular soldiers did.
Perhaps the best-known and easily most distinctive of the Dalek elite mooks is the Special Weapons Dalek, which appeared in the serial "Remembrance of the Daleks". How good are they? Good enough to vaporize normal Daleks.
The shows sometimes have a multiple tier grunt system, such as normal Kelzaks and their red Palette Swap, Kelzak Furies, followed by Styxoids, Koragg's badder (and speech-capable!) versions of the Hidiacs. Blueheads started out as Giant Mooks who led regular Mooks, but started being sent in small groups themselves on occasion. Then gold, spiky ones, imaginatively named Orangeheads by the Rangers, arrived and were even more elite (that first one gave them a lot of trouble, being stronger than Monster of the Week level) until the same Lowered Monster Difficulty problem that affected the blue ones set in.
Mighty Morphin' Power Rangers did this regularly, with So Last Season existing before the changing-teams-every-year phenomenon, with each set of Mooks being considered "elite" as compared to the last, until reaching the standard Mook success rate about five episodes in. Z-putties are elite until the Rangers find out they can just hit the big giant Lord Zedd Z symbol on their chests and the Putties will lose power and shatter (though the fights still last a while because it has to be a hard direct hit). Then Tengas were elite until...they weren't. Power Rangers Zeo's Mecha-Mooks, the Cogs, were equally hyped and actually tougher than Putties or Tengas...but that just meant the Rangers had to actually suit up to fight them. Rita also had a short-lived line of Super Putties who were tougher, stronger, and would pull a starfish and regenerate into two Super Putties if smashed, which forced the Rangers to retrieve special blasters in order to break them. These were not used again because Rita had only so much of the special clay used to make them.
The Kull Warriors in Stargate SG-1 are — watch this — Anubis' Frankenstein's symbiotically enhanced super-zombie cyborgImplacable Men. One episode of SG-1 also showed that some of the Jaffa under Anubis were elite Ninja Jaffa. For some reason, they never showed up again after that episode. Sokar had the Red Guard, who were more heavily armored and fewer in number than the usual grunts. Apophis used them after knocking off Sokar and taking over his territory.
Star Trek: The Next Generation plays with this concerning the Borg. The Borg start out as chump Mooks. The problem is... once you knock off a few of the chump Mooks, ALL of them become Elite Mooks, or at least elite enough that they can kick your ass. New foe, wash, rinse, repeat.
Supernatural: Season 8 reveals the existence of the Knights of Hell, demonic super soldiers that served as Lucifer's chief enforcers. By the present, the Archangels have managed to wipe out all of them, save forAbaddon. Season 9 reveals more about the Knights, including that they were founded, trained, and led by Cain (yes, that Cain) until he — not the Archangels, as it turns out — killed them all for killing his wife, whose love had redeemed him.
In VR Troopers, there were Skugs and eventually the stronger Ultra Skugs. (Ultra Skugs have the same Weaksauce Weakness, though: if two touch, both disintegrate.)
Masked Rider has the Maggots (comic relief stooge villains, used for jobs like distraction and MacGuffin theft) and the Commandoids (used to fight.) Kamen Rider Dragon Knight has three stages of grunt evolution (red normal Mooks, white stronger Elite Mooks, blue flying super-Mooks.)
Dominion has the Powers, the Higher Angels that have joined Gabriel's campaign of extermination against humanity. Not only are they vastly more powerful than the Lesser Angels, the fact that they have bodies of their own and don't need to possess human hosts means that they can slip right past the human defenses designed to detect angelic infiltration.
When the evil Supreme Leader sees Captain EO changing her zombie guards into '80s dancers with his music, she sends in her Whip Warriors, scary robots with electric whips who are immune to his music and the rainbows he shoots out of his hands.
Destroy The Godmodder: Happens mainly in large armies, such as the Grox invasion in the tvtropes session, or the paradox event before that.
Most common monster races for mooks have an elite mook variant. Gnolls have the nunchuk-wielding flinds, goblins have the militaristic hobgoblins and bullying bugbears, lizardfolk have the fiendish Lizard Kings, and orcs have numerous variations.
Any mooks that don't have prebuilt variations can just be made into Elite Mooks by the DM by adding class levels or templates, seasoned to taste.
4E breaks monsters down into tiers of elite-ness. Minions are minor mooks, being just like regular monsters, but die in one hit. Elites are monsters that are somewhat harder than their baseline versions, usually lending to using them as leaders. Solos are double-dose Elite Mooks designed to stand on their own against a whole team of players.
Shadowrun has, among other things, Aztechnology's Leopard Guards, Ares Firewatch Teams, and Renraku's Red Samurai.
Elite choices vary between specialized units tailored for a specific purpose, to simply better armed and more expensive versions of the army's core troops, Space Marines have Veterans, Chaos Space Marines have Chosen, Orks have nobs (elite boyz), Eldar have Dire Avengers (elite guardians), Dark Eldar have Trueborn (elite raiders), Necrons have Immortals (elite warriors), and so on and so on. All the Chaos Gods have daemons like this.
From a fluff perspective, All Space Marines qualify compared to the Imperial Guardsmen and PDF Forces who do the bulk of the Imperium's fighting. The Eldar Aspect Warriors also perform similar roles for their people.
Special and Rare choices in Warhammer. Every army has at least one unit that is effectively one unit of normal infantry, just better trained, better equipped, less likely to run, Spikes of Villainy for the evil races, and with a badass sounding name. Compare Chosen to "normal" Chaos Warriors, Stormvermin to bog-standard Clanrats, High Elf Coast Guard to the High Elf Spearmen...etc. The more intimidating the name, the faster you have to run away from them.
The Bohrok-Kal in BIONICLE. The ordinary Bohrok rely heavily on Zerg Rush to overwhelm their foes. But there are only six Bohrok-Kal, who have unique powers, are intelligent enough to speak, and Dangerously Genre Savvy enough to steal the icon that is the source of the Toa Nuva's powers in order to render them inert.
In most MMOs, there is some form of elite mook to keep the challenge up. Most of the time they will be either mini/sub bosses or named/colored/giant mooks, such as "Deadly spider" for a generic name that you might see, that show up at a certain place or mixed in with the normal mooks.
The Ace Combat games have these in the form of the enemy aces, both individual and ace squadrons such as Yellow Squadron (04) or Strigon Team (6), who in a first playthrough will be flying better planes (until late game when the player can afford better) and are better pilots; in 04's "Shattered Skies" mission the Yellow Squadron are present but extremely hard to hit - actually landing a shot on one will trigger special dialogue and prompt them to retreat. The Mook half partially comes from the fact that these pilots are usually never individually identified (in 04whichever Yellow is shot down at Stonehenge is deemed to be Yellow 4, and Yellow 13's fate is sealed at Farbanti by the player having to shoot down all the Yellows there), but the Ace Combat 6 Assault Records has individual Strigon profiles unlock after you shoot down Strigons in certain missions.
Age of Empires usually had one or two units unique to your chosen faction, as opposed to the generic spearmen, archers and swordsmen everyone had with practically identical sprites. Unsurprisingle, these units would always be the elite mooks, whether it's Spanish Conquistadores, Teutonic Hammer Throwers or Aztec Eagle Warriors.
Age Of War had the heavy cavalry and the infantry Royal Guard units as the Elite Mooks of each race. High and Dark Elves also had their elite archers to compensate for slow unit spawn rate.
Like in examples above, various heavy cavalry and infantry usually fulfilled this role in Age of Wonders. However, the units were anything but comparable for each faction — for instance, the human knight was a lot weaker than the elven one, which was compensated by them having gunpowder troops as ranged Elite Mooks.
Alan Wake had the tough Assault Taken with chainsaws and axes as well as Elite Taken that had extremely thick layer of darkness over them and could turn themselves invisible. Alan Wake American Nightmare also had the Splitters (Taken that would split into two when exposed to light), Taken with darkness grenades and Taken that could temporarily turn themselves into flocks of crows.
Alpha Protocol has special elite soldiers intermixed with the regular mooks. These are visible if one looks closely, as they'll have a gray "endurance" meter over their health meter and are noticeably tougher, more aggressive, and better-armed. Al-Samaad's elite soldiers are notable by their red balaclavas/scarves, while Deus Vult's elites are more noticeable by their body armor instead of generic suits or dark muscle shirts, and VCI elites can be spotted wearing berets and no balaclavas. Some of the more professional elites are harder to notice because they all wear the same uniform (CPA, G22, and Alpha Protocol agents) while others are harder to spot because they have no actual uniform (Russian Mafia and Triads).
The cards sent after you evolve throughout the game. The simplest Club guards only fought with spears, while Spades also had a weak ranged attack. Diamonds had chainsaw-like polearms and fired Roboteching projectiles. The Hearts were not only the toughest, but they had missile-like ranged attacks.
There were also the Army Ants corporals. Unlike their underlings, they didn't have guns, but instead had greater health, more powerful melee attacks and grenades.
Revelations replaces the Papal Guards with the Janissaries, who are even more Kung Fu Proof by being able to survive killstreaks.
3 has the Highlanders/Grenadiers with their giant axes and ability to counter normal attacks, Knife Nut Scouts that can counter disarms or guard breakers and the Hessian Jagers who can counter almost all melee attacks.
All games from II onwards have guard types called "Elite", but ironically these are some of the weakest guards in the game (ranking only above militia).
In Batman: Arkham City, there is a team of Elite Mooks called Tyger, which are the top mercenary group of Ex-Special Forces that were specially trained to go head to head against Batman. Well, in-universe, anyway. They are, most of the time, as easy to defeat as other Mooks. There are also inmates armed with knives (or broken bottles) and electrical sticks, and new enemies using shields or body armor. They aren't exactly elite fighters anymore (any mook can pick up a knive dropped by another one, for example), but they are harder to beat.
Battlefield: Bad Company 2's singleplayer campaign actually points out the presence of Elite Mooks in the loading screen hints before the mission Zero Dark Thirty, warning the player that they are better equipped and have faster reaction time than average troops. They show up about midway through the level, in the form of Kirilenko's green-clad personal guards. They're no more durable than most mooks, but they are, indeed, faster, and carry some weapons that are normally available only to the player.
And the SPECACT DLC lets you become the Elite Mook in MP!
Bayonetta firstly had the Ardors: an upgrade over the basic Affinity angels but still weak, unless they were wreathed in flames. Then there were Joys, which had the similar fighting style to Bayonetta herself and later on Grace and Glory. These had the even tougher Gracious and Glorious appear at higher difficulties.
The Binding of Isaac had the Champion versions of virtually every enemy. These usually were were of a different colour and had doubled health, damage (always a whole heart instead of usual ) or both. Bosses also had Champion versions, but those typically sacrificed one stat or ability in exchange for a different one, and could've been easier, harder, or about the same difficulty as the original boss.
There were also the improved variations of many enemy types. While some were simple stat increases (Large Red Flies) or came at expense of other stats (Red Boom Flies exploding into longer-ranged but less damaging Spread Shot instead of death explosion), others were unquestionable improvements. Examples include ExplosiveLeeches, Angelic Babies (triple Spread Shot instead of normal one & better health) and psychic Maws (fire Roboteching projectiles intead of normal ones).
The Big Daddies in BioShock, which were split into the drill-wielding, melee-only Bouncers, and Rosies, who deployed proximity mines and used rivet guns. There were also Houdini Splicers who teleported around and shot fire or ice, as well as Spider Splicers that avoided attacks by dancing on the ceiling. Later in the games, elite versions of Big Daddies can be found; they are stronger, faster, and tougher than regular Big Daddies.
BioShock 2 introduces Rumbler Big Daddies, which had heat-seeking rocket launchers and deployed mini-turrets. Its Minerva's Den DLC had Lancer Big Daddies with Ion Lasers and Ion Flash. Finally, it had Brute Splicers, which are essentially the Splicer equivalent to Bouncers: they lack the drill and aren't as tough, but are faster, can jump around and throw the objects on the level at you.
The all-red Mooks in the Boktai series that will randomly replace an enemy in a level sometimes. They move around like a bat out of hell, can kill you in only a couple of hits, have tons of HPs, and are better off avoided since you get no rewards whatsoever for actually killing them.
Borderlands gives Elite Mooks the label of "Badass" in front of their enemy type. Your first New Game+ with a character has these enemies labelled Bad Mutha, a second time labels them as "Superbad". In the sequel, they're generally known as "Super Badass" or "Ultimate Super Badass".
In The Chronicles of Riddick: Assault on Dark Athena, the Mercs in red armor with red googles encountered towards the end of the game are insanely well armored (taking almost a full clip of assault rifle fire to kill), but most players won't even notice since by that point in the game you're given a One-Hit Kill rifle with unlimited ammo.
Every long-running enemy group in City of Heroes has these (the Council goes from random raw recruits to elite special forces to enhanced super-soldiers to superhuman monstrosities and robots).
Command & Conquer Generals has the USA faction comprised entirely of these. The basic infantry, air and tank units are the US Army Ranger (the only infantry that can clear houses) F-22 Raptors and M1A2 Abrams (called the Crusader in the game), which are all superior, but more expensive than their nearest counterparts.
The main Command & Conquer games had the NOD Black Hand as one of these, being tough, disciplined and equipped with flamethrowers, while the GDI has Zone Troopers soldiers in Power Armor.
In Condemned, the so-called Oro appeared in game's finishing levels. These were humans who had their larynx replaced with metal attachment, allowing for ultrasonic attacks on top of their elite weapons and training. Earlier on, any enemy with a gun acted as one when compared to other homeless with crowbars and bats.
The Bratgirls from Crash Of The Titans, which have a lot of health (Although the dropkick can still kill them in 1 hit) and can do a lot of damage with their attacks, especially their megaphone attack which also dizzies you. In Mind Over Mutant however, they have been significantly downgraded, not having nearly as much health and doing much less damage.
Cryostasis Sleepof Reason had the firearm-using monsters appear more frequently later in the game, including a parka-wearing giant who dual-wielded PPSh submachineguns. There were also the extremely tough frozen spider enemies and the once-humanoid monsters that have grown moth-like wings.
Dark Souls has the Balder Knights (also known as Elite Undead Soldiers) starting from Undead Parish. While most Undead Soldiers you face so far aren't much of a threat, Balder Knights intend to shock newbies into a much more careful playing style, as the swordsman-type Knights wield their iconic Balder Shield with rapid attacks from their Balder Straight Swords, while Fencer-type Knights are even faster, and is able to parry you, with usually disastrous consequence if they do. In NG+ onwards, stories of Balder Fencers one-hit-KO-ing experienced, but careless players abound.
Hollow Undead are even more of a pushover, especially past the first few levels. Come to Duke's Archives, and you'll be greeted with Crystallized Hollows. Heavy defense against physical attacks, nigh-invulnerable to magic, and usually backed up by Status Buff-capable Channelers, themselves an example of Boss in Mook Clothing. Due to the narrow walkways of the Archives, getting sniped by a powered-up Crystal Hollow Archer can instantly kill you, especially when you have your back exposed from fighting others.
Dead Space had the Enhanced versions of all its Necromorphs: these were always jet-black and much tougher than the normal ones. It also had Twitchers, which behaved much like Slashers, but were unnaturally fast due to the Stasis implant getting digested wrong by the Necromorph organism.
De Blob had the Inkies equipped with rocket launchers, which were pretty much the only enemy type that presented a decent threat to your character, mainly because the Knockback could sent him straight down the Bottomless Pits.
Descent had the Hulk series of robots. Small Hulks and Medium Hulks are standard mooks, but the normally-brown Mediums have a Palette Swap: the Red Hulk. This guy was the bane of many players of the game, as he had three times the health of a normal Medium and fired Homing Missiles as well. A very common foe from mid-to-late levels. (And the Red Hulk's elite version, the Fusion Hulk, was a full-blown Boss in Mook Clothing.) Class 1 Platform robots were a mere nuisance, but the green variety fired triple missile bursts rather than lasers, making it extremely dangerous. And finally, both Medium Hulks and Class 1 Drillers had cloaked versions, which in the Driller's case actually had more health than the standard in addition to being invisible.
Literal elite monsters in the Diablo series, which was handed down to its spiritual successor World of Warcraft. They have a golden border around their portrait and are much tougher than their normal counterparts. How much more depends on the setting. Outdoor elites might be killed by a single character of the same level, although it's much more difficult, while dungeon monsters are designed to be a threat for a full group or even a raid (up to 40 players).
The players themselves could be a form of this. Raid dungeons consist of a group of 10, 25, or 40 players. Many of the raids feature the raiders as a small but powerful strike force clearing the way for the standard soldiers to get through.
Each of Devil May Cry installments had these: from Secretaries in Devil May Cry 3 to Dream Runners in DMC remake.
Dishonored had the Watch Officers, which had helmets (made some headshots impossible) , better fighting skills and pistols. Overseers then appear as elite mooks to all Watch Guards. They always had better fighting skills, carried either pistols or grenades with them and had the full face-protecting masks. There are the infamous Tallboys, which were immune to just about everything and had great health. Finally, Knife of DunwallDLC added Butchers with huge circular saws that dealt insane damage with them and could fire bone chips (or something of a kind) from them as a ranged attack. A shot to the fuel tank would take them out, but they could also deflect projectiles with their blades!
The game also has a fair share of Superpowered Mooks. There are Music Box Overseers, which disabled all Corvo's powers with their music, could generate Shockwaves and could only be killed by leg or back attacks due to music boxes themselves being bulletproof. Then the Daud's Assassins, which teleported around, threw knives at you and had great fighting skills. Finally, Brigmore's Witches had the titular witches, which, amongst other spells, had damaging screams, could drain life from you and whose elites summoned roots from the ground to trap your character.
The Arch-Viles of Doom are Elite Mook that can summon or resurrect lesser mooks. There also the invisible demons and Hell Knights. Doom 2 has Arachnids with plasma cannons, chaingun-using zombies, the demon with two simultaneously-firing guns and more.
The Darkspawn Alphas, which often act as mini-bosses. Interestingly, genlocks, which were the weakest darkspawn in-universe, had the most interesting and challenging Alphas. While Shriek and Ogre Alphas only had boosted-up stats on their side, and Hurlock Alphas were no different from humanoid Two-Handed captains, Genlock Alphas had many extra skills, and the archer variety knew the entire skill tree, being the only archers in the game to do so.
Similarly, any enemy with a name highlighted in yellow was usually an elite variety. For animalistic monsters this only meant boosted-up stats, while human and demon enemies typically had extra skills on their side. Most common human Elite was either a Heavily Armored Two-Handed mook or similarly heavily-armored shield-using Champion.
Any enemy with a specialisation, whether Berserker, Assassin or Arcane Warrior, was always going to be one of these.
Dragon Quest I's final dungeon is guarded by the deadliest, most demonic variations of the Mooks you've faced: Axe Knights, Armored Knights, Blue Dragons, Red Dragons, etc. They have high defense stats, deal massive damage, and have the most devastating spells, such as Sleep (Axe Knights have both this and Stopspell, preventing you from using your own Stopspell), Healmore and Hurtmore (the Armored Knight has both Healmore and Hurtmore). If you aren't sufficiently leveled up, you can kiss your ass goodbye here. Some of these are invincible to magic. And sometimes, the only winning move is not to fight.
In Dynasty Warriors 6, enemy generals will sometimes be accompanied by nameless Lieutenants. This can lead to the odd situation where you curb stomp the general himelf, and then immediately find yourself getting slapped around by his elite goons.
Dynasty Warriors 8 has "Mobile Unit Captains" and "Unit Commanders" that have slightly more health than foot soldiers and, visually, are only distinguishable by their having titles over their heads and by the Unit Commanders having BFSs.
Skyrim has Forsworn Briarhearts and Draugr Deathlords, who can take off a good 60% of a mage's health with one melee hit. If you meet one of the latter early on and you have a follower, expect the worst.
Tom Clancy's End War has them. How? The player's army, stated to be the best taken and bunched up from all the other elite forces of their root military, and The Cavalry commonly in other circumstances.
Eternal Daughter had some of these. There were the elite Dungaga soldiers, including ones with shields and more advanced wild-roaming enemies, like the skeletons that would throw bones at you.
The Genedisruptor Parasites in Evolva. Appearing only during the two last levels, not only they are significantly larger than any other mook (to the point that their small version is about the same size than standard mooks), but they can also take a lot of damage, and their main attack is a beam that drains life fast and confuses your Genohunters (if the affected Genohunter is the one being controlled, it inverts the controls; on non-controlled Genohunters, it makes them start attacking each other).
The Fable games have these. The first has the "Minion" monster, large armored monstrosities that can give even an experienced fighter a run for his money.
Fable II has the Spire Guards. justified, as most spire guards are either mercs hired from champions of The Crucible, or just have their memories and identity ripped apart and become unthinking brutes.
The regular, non-Behemoth Super Mutants in Fallout 3 come in three kinds: Super Mutant, Super Mutant Brute and Super Mutant Master, each one with ascending HP and weapon capabilities respectively. Plain Super Mutants aren't armored, Masters are all armored, and Brutes are both armored and unarmored. Broken Steel adds a fourth rank, the Overlords, who have HP approaching that of a Behemoth and wield BFG's such as Tri-Beam Laser Rifles and Gatling Lasers. For the hostile humans, there's the Enclave soldiers, who wear Powered Armor and often wield heavy weapons such as lasers or plasma rifles. Broken Steel also has Hellfire soldiers, with fire-resistant armor and Heavy Incinerators.
In Fallout: New Vegas, the major factions have their elite mooks as well. The NCR has Veteran Rangers, who use high-end firearms like the anti-material rifle and are heavily armored, and the Heavy Troopers, who use big guns such as miniguns and stripped-down versions of Brotherhood of Steel armor. Caesar's Legion meanwhile has the Centurions, who command other forces of the Legion in battle and are equipped with the best weapons that the Legion can provide and the Praetorian Guard, who use high-end unarmored-class weapons.
Far Cry had the invisible mutants that could only be seen through the night-vision goggles and the tall, rocket-launcher wielding mutants. In Far Cry 3, this overlaps with Heavily Armored Mook. The "Heavy" enemies wear high-grade bulletproof masks that take entire clips to shoot off, while the Flamer enemies have even more armor and are immune to fire. This makes them extremely hard to snipe, but the Heavies don't cover the backs of their heads, and both enemies can be susceptible to a simple Takedown if you select a specific Heavy Takedown skill.
Goblet Grotto had a parody of this with the Ultra Skeletons, which had unnaturally thick rib cages and could be observing knitting extra bones into their chest to keep it up. However, they were no different from regular skeletons and still died in one hit. One skeleton also discussed the Sorting Algorithm of Evil as typically faced in strategies.
God of War had these in every game. The most famous examples are probably the Satyrs from God of War 3 and Sirens from Ascension.
In God Hand, there are two basic elite types: the "tall" model and the "fat" model. Both are much harder to send flying and have a lot more health.
GoldenEye often broke out the Elite Mooks during a high-alert situation, for example, in GoldenEye, once the Scripted Event alarm goes off after hacking the mainframes in Severnaya, endless waves of smart, quick, heavily armed elite guards are spawned (get out of there!).
Grand Theft Auto has the more elite policemen appear once you receive three or more stars. Firstly it's the SWAT in body armour and equipped Uzis, which arrive in helicopters or police trucks. Then come the extremely tough 4-wheel drives which carry four of the dreaded FIB, whose MP5s make mince meat out of the Player Character in seconds (this step was removed in Grand Theft Auto V). Finally, you have the military with long-range assault rifles and which will show up on tanks.
Grand Theft Auto: San Andreas also had similar levels during the battles for location dominance against other gangs. First wave has thugs equipped with same pistols and Uzis they always have. Second has shotguns and better guns. Third wave is equipped exclusively with AK-47s.
Guild Wars: In Prophecies, the Mursaat fill this role compared to the white Mantle. In Factions, Shiro'ken are elite mooks compared to afflicted. In Nightfall, Margonites (and torment demons to an extent) act in this role compared to normal Kournan soldiers.
Combine Elites in Half-Life 2, who wear white uniforms instead of the grey and black variety found in others, and have weapons with an "alternate fire" mode which can instantly disintegrate NPCs, whether Red Shirt or Mook, are a mixed bag. In-Universe, they are a straight example, but in gameplay terms, they're closer to Fake Ultimate Mook: the dreaded pulse projectile only deals 15 damage to Gordon, they can't throw the grenades the ordinary Overwatch soldier is known and feared for using, and their health is negligibly higher than normal Overwatch.
The aptly-named Elites of Halo, the strongest forms of which are the black-ish-armored Spec-Ops types, who were the only Elites who used grenades in the earlier games (and boy, did they throw fast), and can turn invisible in the later games; the white-armored Ultras with their insane durability (up to four or five sniper shots to the head in the highest difficulties), quickly-regenerating shields, Guns Akimbo, and instant-death Energy Swords; and the Zealots (gold armor in the original trilogy, maroon since Halo: Reach), who, depending on the game, can combine together any of the aforementioned features. These elite Elites (heh) also shoot faster and more accurately than their lesser comrades, and are much dodgier to boot.
Other elite Elites (heheh) are the jet-packing Rangers, the gold-armored Generals in Reach, and the also-golden Warriors from Halo 4.
Their Evil Counterparts the Brutes are also this, the most powerful being the Brute Chieftains, who are heavily armored and shielded, wield either Gravity Hammers or a super-heavy firearm, equipped with temporary invincibility shields, and can take about three grenades to the face on the highest difficulties before dying (if you could even make the stick, since in their earliest appearances, plasma and spike grenades would merely bounce off their armored sections). Other elite Brutes include Captains, Bodyguards, and Jumpers.
The higher-ranking Skirmishers (Murmillos, Commandos, and Champions) in Reach are both very durable and insanely agile; to make things worse, the Murmillos will use their dual arm-shields to prevent headshots.
Even the Grunts have their elite variants in the Spec-Ops, Heavy, and Ultra Grunts, who were experts with grenades and BFGs (and could even use the basic plasma pistol well), and the Ultra's Halo 4 replacement, the Imperial.
Halo 2 also had Sentinel Majors, gold Sentinels with more powerful blue beams who were the only variant to have shields in that game.
Halo 4 has the Promethean Knights, large mechanical warriors who can teleport across the field, are armed with fairly heavy weapons, and can be revived by Watchers. To top it off, they have their own elite models in the Lancer, Battlewagon, and Commander.
In FAMOUS had the more elite soldiers sent after you in the later parts of the game.
Iji had the Komato Berserkers and Assassins as the elite varieties of simple troopers. The former had great health, carried powerful Shocksplinters for ranged attacks and Resonance Deflectors up close, and would reflect the missiles in front of them back at you. The latter had a lot less health, but teleported around like crazy, had great variety of powerful moves and would reflect explosive projectiles regardless of direction.
Judge Dredd Vs Zombies had the bloated zombies that exploded at death (and could take other zombies with them, too), extremely tough "old man" zombies that survived ungodly amounts of punishment and the "leaper" zombies that would frequently make 2-3 metre jumps to get at your Judge.
Kane And Lynch 2 Dog Days had the Chinese riot police and military. Not only did those have advanced shotguns and assault rifles, but their body armour actually gave them more health than the player characters.
Killer is Dead had the gold-plated Wires appear about halfway through the game and become more common from there. These were much tougher than usual and often could only be killed while in the Adrenaline Rush mode.
The first Killzone had the minigun-wielding troopers and nothing else. Killzone 2 introduced the flamethrower troops and enemies with grenade launchers alongside varieties of more basic mooks. Killzone: Shadow Fall had scouts with radios who would summon support to them and the troops with shotguns and riot shields.
The rare Nightmares in Kingdom Hearts 3D are simply a white Palette Swap of the usual nightmare types, but have much higher stats, to the point where it's tough to cause more then Scratch Damage to them initially, plus they can always take a sizable chunk out of your health, even if you're considerably higher in level then them.
The Last Stand had various heavily armored zombies (including [[Shield-Bearing Mook riot police zombies that could only be shot in the feet) and very fast zombies, as well as zombies smart enough to use actual weapons, including firearms.
The Last of Us has Fireflies in its final level. Unlike all other human enemies, they are equipped with proper military-grade body armour and assault rifles (as well as some of your own weapons they took earlier). It is possible to sneak past them, though it's questionable as to whether you would want to.
The Uncommon Commons of Left 4 Dead 2 are Common Infected but with perks that make them tougher than average: Riot Infected in body armour that make them bulletproof everywhere except the back, Hazmat Infected in fireproof biohazard suits, Mudmen who crawl on all fours, move quickly in water and can blind the Survivors with mud, Clown Infected whose squeaky shoes and noses attract other nearby zombies, and Worker Infected who won't follow pipe bombs/bile jars because they wear ear protection.
The Lord of the Rings Online has signature, elite, elite master, and nemesis versions of mooks, each progressively more dangerous. Signatures can be found on the landscape; nemeses, with over 20 times normal health, are confined to raid dungeons, but are still nameless mooks.
It's not really that indicative, though, at least between Elite Master and Nemesis. The player is about equal to a signature in health (less for some classes, like lore-masters), but are pushed up to about the strength of an elite by their advanced human brains and their much larger array of moves. A normal enemy has about 50% of your hitpoints and a swarm has about 25%. Generally, each level is about twice as powerful as the last, up to Elite Master. The line between Elite Master and Nemesis is INCREDIBLY blurry. In the first part of the Great Barrows, a 6-man instance, you fight an Elite Master who's REALLY tough, and you'll probably be wiped out several times. In the 6-man version of the fourth skirmish, Thievery and Mischief, you fight three nemeses at once as a boss with relative ease.
Lord Of The Rings The Two Towers and Return Of The King tie-in games had Uruk-Hai as the general Elite Mooks to weaker Orcs. They had the heavily armored variants, the crossbowmen (which dealt much greater damage at range than Orc archers and could throw fire bombs) and the Berserkers. Those dealt plenty of damage, had greater attack range than the player because of their scythes and could block most of your attacks and rapidly counter-attack.
The three mercenary gangs in the same game also had these. Blue Suns had the relatively weak Legionnaries and Centurions, who were tough but were equipped with slow-firing Vindicators. Eclipse had far more dangerous Engineers and biotic Vanguards, which were able to deploy drones and Ao E attacks. These had more elite Operatives and Commandoes. Finally, Blood Pack had Krogan Warriors as its Elite troops, but they were slow and restricted to short-range shotguns, making them little better than their Vorcha Underlings.
Cerberus in Mass Effect 3 has this in the form of the Nemesis and Phantom units, elite specialists designed to work perfectly in tandem with one another: while one keeps you pinned down with the threat of sniper fire that can instantaneously destroy your shields, the other closes the distance so they can insta-kill you with their fancy swords. Phantoms also have the benefit of crazy-powerful handguns that can kill you long before they close the distance if you don't take cover, in addition to cloaking devices and fancy acrobatics.
The Reapers have their own variants, in the form of the Brute, a monstrosity with the body and strength of a krogan, and the head and intelligence of a turian, which results in lethal efficency, the Ravager, a rachni husk, repurposed to bring heavy fire onto enemies, and have it's babies brainlessly swarm you, and, worst of all, the Banshee, a Reaper-fied Ardat-Yakshi asari, who can hit you with an attack that deals damage to you over time, biotically rush you, pick you up, and gut you with their long claws that would make aWitchjealous, and get their name because of their pants-wettingly horrifying scream. In the early stages, Marauders are built up as this, playing the role of coordination/enhancement units for the basic cannon-fodder Cannibals, but literally the next stage of the mission where they're introduced lets you meet your first Brute, and Marauders are instantly relegated to being little more than Cannibals with shields.
The Matrix Path Of Neo has the Master Vampire in the club that can teleport around the room, move even faster and is stronger than the normal vampires.
Along with the Witch Queen who has Gravity Master powers, can teleport and has telekinesis. Where as the regular witch only has Blow You Away powers.
Max Payne 3 had the enemies clad in advanced body armour and helmets at the end of the game. These were tougher than the player and required more than one headshot to kill.
Starting with the fourth mission in Medal of Honor: Frontline, you encounter elite mooks with body armor who can take twice as much punishment as the normal mooks.
The latter half of Mega Man X 8's final level gives us mass-produced copies of Sigma.
Mercenary Kings had the incendiary and electrical versions of basic CLAW enemies (Patrol, Guard, Shield Guard) that have much greater health (particularly electrical ones) and inflict bonus damage of their element with each shot. There also similarly elite electric turrets, which have double their already considerate health and damage.
There are two further elite versions of Shield Guards. One is Abductor, which is tougher and uses hostage as a shield, which means you have to get behind them if you don't want to lose bonus points. Second version is Charger, which doesn't shoot, but is very fast and runs at you in melee with a spiked shield.
Many Metal Gear games have several elite enemy soldiers in addition to the regular kind fought by the player throughout the course of each game.
The original Metal Gear Solid have the Heavily Armed Troops, who wear full body armor and helmets. They are specifically said to be former members of Big Boss' elite guard (rather than VR-trained novices like the rest) and thus they have more hit points than the other troops.
Metal Gear Solid 2 has the Hi-Tech Soldiers, who are members of Solidus Snake's private guard and appear only during the alert phase during the latter half of the Plant Chapter (specifically after Raiden contacts Ames). Later, when the player reaches Arsenal Gear, they'll encounter the Tengu Commandos, who are armed with ninja-like gear.
Ridley's "Ninja Space Pirate bodyguards" in Super Metroid.
Mirrors Edge had the Anti-Runners, which were specifically trained to deal with Runners like you. As such, they could easily keep up with you, dealt great amount of damage and were immune to many of your moves.
Ninja Gaiden, which places Bad Ass super-ninja Ryu Hayabusa and Fiend-Hunter Rachel in the Vigoor Empire with the task of killing everything around them. The game expands upon the genre staple of tough, then tougher, than tougher monsters by arranging a pattern of leadership for all enemies, human, fiend, and mechanical.
Ninja Senki had the Green Ninjas, which could alter their shuriken trajectory depending on your position and jumped up when throwing it to make it harder to hit them. There were also the Purple Ninjas which jumped around like crazy and could practically Goomba Stompyou and the blue-colored demon heads, which gained a projectile attack in addition to their mobility.
No More Heroes 2 has the katana mooks, which have considerable health and actually know how to counter your attacks. Then there are the rarer laser katana mooks, which are tougher, more skilled and deal a lot more damage. Finally, there are the chainsaw-wielding fat mooks, who don't block, but can take a lot of punishment before they flinch and can carve huge chunks of health out of Travis' life meter.
While it's difficult to ascribe normal gaming tropes to Pathologic due to its extreme realism, it still had several powerful variations on normal enemies. The arsonists you encounter at one point will throw their fire bombs that deal significant damage over time and some bandits will throw knives with extreme accuracy. Finally, if things go really wrong, the rebel soldiers will appear as the only other entities with firearms.
Near the end of the Datadyne Extraction level in Perfect Dark, Cassandra kills the lights and you have to fight her Bodyguard Babes (who have night vision goggles) in the dark, which is quite frustrating on Perfect Agent difficulty. PD also has the Datadyne Shock Troops (better health, better AI, and sometimes better weapons) and female Datadyne guards (better AI and almost always better weapons).
Plants vs. Zombies had many special zombie varieties. Amongst many others, there was the Pole Jumper Zombie that would bypass the first plant, Football Player zombie, Balloon Zombie, digger zombie that would destroy your defences from behind and Ice Machine Zombie that rolled over your plants and created pathways for bobsled zombies.
P.N.03's Pilz, the most common mook, have several palette swaps, each tougher, more agile, and more intelligent than the previous. Additional sub-variations are armed with missile launchers or plasma cannons.
In the Pokémon games, after going through enough Team Rocket (Magma, Aqua, Galactic...) Grunts, you may run into an Executive, who often serves as a miniboss of sorts.
Better examples are in the Pokemon Ranger games, where the original has Elite Mooks, the sequel has Mook-like Admins with higher ups, and Guardian Signs has two levels of admin.
Team Flare fits the bill much better than previous teams, as its Admins are a generic class just like grunts; it's the scientists that are unique.
A somewhat different definition of 'mook', but Ace Trainer (Cooltrainer in earlier generations) class NPCs often appear in Victory Road and other high-level areas and use tougher Pokémon and superior tactics to most generic trainers. Their Japanese name is "Elite Trainer".
"The walkers" are this compared to "Infected Citizens". Unlike other examples of this trope, The walkers aren't threat to Alex even in large groups.
Prototype2 has the Brawlers for the Infected, the Orions for Blackwatch, and eventually the Evolved
Story-wise, some of the terrorists in Tom Clancy's Rainbow Six Vegas are ex-Special Forces mercenaries, while others are simply Mexican criminals working for Irena Morales. However, in-game, there's no actual distinction between the groups, as they both use the same set of character models and uniforms, as well as the same A.I. and equipment.
In Rayman Revolution, the robotpirates got steadily more elite depending upon colour scheme: from weakest to meanest, it goes green->purple->yellow->red->those idiots in barrels. (They get steadily less elite as your main attack gets more powerful, however.)
Red Faction 2 is an interesting case, as Elite Mooks are fought in the very beginning of the game(the prologue mission), and oddly disappear completely after the first few levels, where they're replaced by weaker, but more heavily armed, standard infantry. These "Sopot Elite Guards" wore metal armor and faceplates, could survive about twice as much damage as a standard Mook, and talked like Darth Vader. They make a comeback at the end of the game as Elite Nano Soldiers.
The originalRed Factions Elite Guards, first seen in the Administration level, and later in Capek's lair and other high-security areas, had a different voice, spoke more aggressive catch phrases, moved and dodged faster and had much tougher armor than the standard Mooks. They also frequently wielded various BFGs.
Remember Me had the Prison Enforcers, which were largely the same, but could perform a Brain Lock grappling attack and Reconversion Leapers, which were tougher than common Prowlers and immune to several of your skills. Then, there were Heavy Enforcers, Strangler Leapers that could become invisible at will and the aptly named Elite Enforcers, which had the electrical armour that damaged you with every blow you land on them. Since the game has no Regenerating Health, this requires the exclusive use of health-regenerating moves on them.
Resident Evil 4 has the Ganado Militia, which inhabit the Final Dungeon and are more intelligent, faster, and better armed than other mooks. Some wield large hammers, rocket launchers, or Gatling guns.
In Rise of the Kasai, enemies wearing armor count as this; they're the same as normal enemies but are impervious to arrows, and take a few more hits to kill. Depending on which weapon you're using at the time and how lucky you are, "a few" can translate to "one" for a grand total of two hits.
Ryse: Son of Rome had the enemy squad leaders, which had better fighting skills and required more elaborate combinations to defeat.
In The Saboteur, we get the superior Nazi soldiers who use very powerful weapons and armor. Lucky for you, you get to use these weapons too.
Each enemy group in Saints Row: The Third has its own particular Elite Mooks with unique weapons. Morning Star has sniper duos in helicopters, Luchadores have enemies with grenade launchers, Deckers have the agile, teleportingAlice expies with Shock Hammers, and the police use either snipers in helicopters or riot police. STAG's Elite Mooks carry the same laser rifles/shotguns as their basic soldiers, but are even heavier armored, and are the toughest troop in the game by far.
The Syndicate gangs will also throw out Brutes, which take a lot of damage to kill, can dish out a lot of it in return and will flip cars and obstacles around with ease. They can also potentially come armed with miniguns or flamethrowers. On the bright side, you get a Finishing Move for them that lets you stuff a grenade in their mouth, and flamethrower ones are subject to Flamethrower Backfire.
Saints Row IV's equivalent of Brutes is the Wardens, who are spawned either during missions, while clearing Flashpoints or Hotspots, during training simulations or simply by getting six bars on your notoriety. They have high health, are typically protected by a shield that requires you to use your superpowers to briefly disable it and have various superpowers of their own. There also are lesser varieties of elites, such as the Specialists that also have Super Sprint and Jump, the durable and grenade- or minigun-wielding Murderbots, or the immune unless you Attack Its Weak Point Marauders.
Throughout all the Saints Row games, your named Homies can be this, as they're generally tougher than random Saints members picked up off the street. In The Third you also get a Brute of your own in their unwilling progenitor, Genius Bruiser Oleg.
The Macintosh game Sensory Overload had, in its later levels, elite guards who looked like Nazi officers and wielded machine guns, and cyborg soldiers who talked like Darth Vader and threw plasma balls (the same projectile as the Electrogun). The unnamed female Dragon and Final Boss was a slightly enhanced (faster, and with a melee attack) Palette Swap of the cyborgs, ie a type of King Mook (or queen mook, if you will).
Serious Sam had many such enemies. There were Beheaded Bombers which threw grenades non-stop and Beheaded Firecrackers, which were just like Beheaded Rocketeers but fired a Spread Shot of five instead of a single one. Adult Arachnids had a lot more health than Juveniles but were very rare. Finally, Biomechanoids Major were much tougher than Biomechanoids Minor and fired much more powerful missiles instead of lasers (though missiles were destructible).
The Zorg Troopers and Commanders act as such to Beheaded Rocketeers and Firecrackers. They're still weak, but they possess doubled health, movement speed and fire two shots in a row instead of one (Commanders have double-damage Spread Shot lasers instead.)
Shrek the Third had the knights as armored and improved mooks. Both them and pirates also had shield-bearing elites. The prisoners also had sharpened-spoon-wielding elites that performed some acrobatic spin attacks with them and dragonlings had high-flying elites that could only be hit when they descended to attack. Finally, there were elite witches that summoned impenetrable force fields around them and required containers thrown at them to break through.
The early games in Silent Hill series feature tougher, faster, Palette Swap (or not) versions of the enemies in certain areas (or when you're sucked into the mirror version of the town/area). For example the Night Flutters (Air Screamers, but more human-like and with their faces covered in worms), Worm Heads (upgrade of Groaner, the ubiquitous zombie dogs, but with a worm for a face), and Shadow Children (transparent version of gray children) in SH1, "nightmare nurses" in SH2, and "advanced Closers" in SH3.
Before the trend largely came to an end with Silent Hill Origins and following games, Silent Hill 4 had several prominent examples. There were "New Type" Gum Heads with greater health and frequently equipped with golf clubs. The dog-like Sniffers had more powerful Females and the Leeches in the Water Prison got a slightly tougher red variety.
Singularity had the better-armored and equipped Soviet soldiers appear later in the game, including ones with riot shields. Then, there were the Zek mutants, which were much tougher than regular zombie-like creatures and more advanced ones could become invisible.
The first Soldier of Fortune had the Order Troopers, and Double Helix had the Prometheus operatives. In Payback, the Big Bad's elite minions wear body armor similar to Rainbow Six agents, and like all mooks on the final mission, inflict much more damage than in previous missions, and can easily kill you in one hit on Hard difficulty.
The 33rd Battalion in Spec Ops: The Line had the Zulu Squad appear late in the game, whose members had advanced body armour and some of the best weapons.
The second-to-last level in Splinter Cell: Chaos Theory ended with Sam up against Shetland's personal bodyguards, about 8 elite Displace Mercenaries equipped with facemasks and thermal goggles. These used to be the only enemies in the entire series who could see you in the dark (some enemies in the series, i.e. the Georgian Special Forces from the final mission in Splinter Cell, wear night-vision goggles, but still couldn't see you in the dark unless you move or are very close). Then came Conviction and the enemy Splinter Cells, who had sonar goggles that let them see Sam's Last Known Position through darkness and cover. Blacklist only ran with it.
S.T.A.L.K.E.R.: Shadow of Chernobyl has Spetsnaz special forces soldiers and Military Stalkers, who have the two best non-exosuit armors in the game.
The general trend of late game introduction of elite mooks is subverted in STALKER - the player can encounter Spetsnaz in the first area of the game, in the Cordon by the Military Guard Post. Approximately two to three hours later, the PC can encounter them in Agroprom Research Facility if they hang around too long around after rescuing Mole from the military. At both times a PC will likely have a low end assault rifle/sub-machine gun and armour, leading to a quick death if they don't flee.
In general, within the games, any mook wearing a SEVA suit or Exoskeleton is this, reinforced with their high-end weaponry.
The Monolith faction is comprised almost entirely of them, as they have access to almost all of the weapons in the games. This includes the deadly Gauss Rifle.
Starcraft has elite versions of normal units, such as the Zerg Hunter Killers. These are buffed up Hydralisks with twice as much health and firepower as any normal Hydralisk.
The sequel takes this further, with mercenaries who not only have better damage and health to start with, and benefit from upgrades researched in-game, but in the single-player campaign armory and lab upgrades apply to units of the appropriate type as well, so Hammer Securities troops you pick up benefit from your Ultra-Capacitors, Vanadium Plating, Concussive Shells, and Kinetic Foam, as well as any of your bunkers' Neosteel Frames and Projectile Accelerators.
The Suffering had the much tougher Slayer Captains appear halfway through the game, alongside regular Slayers requiring decapitations to stay down for good. The Suffering: Ties That Bind had Slayer, Burrower and Arsonist Captains, which required the use of Torque's monster form to be destroyed.
Time Crisis's red-uniformed enemies have near 100% accuracy, making them Demonic Spiders. At least you get a warning when they're about to fire in 2 and beyond. In the first game, Sherudo and Wild Dog have white-uniformed bodyguards. There are also the heavy weapons soldiers(with machine guns, rocket launchers, and flamethrowers), and the gray commandos (second to the reds) in the later games.
Time Shift had cybernetic Quantum Guards, who possess the same time-bending powers as the player.
In general, the more evolved units of each type (artillery, gunners, spearmen, light infanty, heavy infantry, light cavalry and in some games heavy cavalry + archers) are this to their basic versions. For instance, the Armored Sergeants in Medieval 2 Total War are Elite Anti-Cavalry mooks, while the unique English Sherwood archers are Elite Archers, etc.
Later in Valkyria Chronicles, the enemies become tougher and become labeled "Elite", the black-clad Imperial Guards even more so.
There are also additional units during the main campaign called "Aces", which are named and are tougher than the standard Imperial soldier. Defeating one in combat will allow you to get a unique enemy weapon after you win the battle.
Typically, the 2nd or 3rd in command of a gang in The Warriors will fall under this trope, having more health and strength than the common mook.
In the Wing Commander series, most of the games have the elite opponents either named and with personalities, flying unique ships, or both. The exceptions:
The Drakhai, in Wing Commander II. Slightly better defensive stats for their ships, and an AI set one level above the regular opponents were the primary distinguishing characteristics, aside from their specific taunt "You cannot defeat the Drakhai" (ignoring that you regularly did just that).
In addition to the few named opponents (other than Seether, which ones depended on when you defect, Wing Commander IV also had nameless, generic "ace" pilots.
Most enemy types in the Wizardry games start off as regular Mooks, but upgrade to Elite Mooks in higher level areas, then eventually to Superpowered Mooks. Not to be confused with the actual Mook race in the game, which are approximately high-tech psychic Wookiees.
Wolfenstein2009 had the the Powered Armor Nazi troopers who could only be defeated by having the two lamps on their back shot. Then, there were elite mutants, including one that was completely invisible.
The Terran State in X3 Terran Conflict has the AGI Task Force (ATF) Elite Mooks. The ATF have their own fleet of entirely unique ship designs, carry ridiculously powerful missiles for their missile frigates, and ATF ships will never bail out or surrender. Other races typically have their plain "Military" ships making up their Elite Mooks - if you were to attack the Boron, for example, you'd mostly be attacking their poorly armed Police and Border Control ships before the military shows up with much better equipped ships.
In Combo Factory, there are the red stick figures, which stand out because of their bright color. They have more health, use more elaborate attacks, and behave more aggressively than the standard stick figures.
Starting from second installment of Heroes of Might and Magic, some non-neutral units could have been upgraded, giving them better statistics, slightly altered appearance and sometimes completely new abilities that made a vast difference between them and the basic version. Green Dragons from the same game take this trope a level higher and can be upgraded twice from Red to Black Dragons. In III, V and VI all non-neutral units became upgradeable.
Tears to Tiara 2 has the emperor's praetorian guard legions, both in game and in story. If not careful they can take out a tank character in two or three hits.
In XCOM: Enemy Unknown, your soldiers will eventually start facing Elite Mutons and Heavy Floaters, the tougher and more heavily-armed versions of the Mutons and the Floaters, respectively. The Elite Mutons are described as the Etherials' Praetorian Guard. They carry Heavy Plasma weapons and use them like rifles.
The Madness Combat series features the Agents, starting in the fourth one, where he manages to stall the protagonist... for a few extra seconds. He gets his revenge, however, later in the episode, when he's resurrected as a zombie, and manages to shoot the protagonist. In the fifth through seventh ones, however, they become as common place as regular mooks, until another elite group takes their place as as Elite Mooks. The three appear in the sixth and are quickly killed, and in the seventh, they're highly commonplace.
Likewise, the Bunnykill series features two ninja rabbits as Elite Mooks in the first installment (and are actually challenging), bunny 'agents' in the second (the first two are challenging, but then about ten are cut down easily in a display of Katanas Are Just Better), and the dark-grey (mercenary) and brown (techie) rabbits in the third installment (the techs provided extra challenge, the mercs not so much).
Red vs. Blue features, in the ninth season, Sharkface, a flamethrower-wielding soldier who manages to give a couple of the top Freelancers a tough fight. Lampshaded by Wash when he first appears: "What the fuck is with this guy?" Later in the same mission, a few jetpack-equipped soldiers prove a challenge.
In The Gamers Alliance, the Blessed are the Master's most fearsome Totenkopf minions who have the authority to command lower-ranked Totenkopfs. The Coalition's S-Class Mullencamp are an even deadlier group of regular Mullencamp who are efficient warriors and mages surpassed only by the Vulfsatz in effectiveness. Demons of Hoch class, particularly the Black Death squad, are surpassed only by the Dreadlords and the archdemons in raw power and cunning.
The Fire Nation had the Yu Yan Archers, who combined Improbable Aiming Skills with ninja-like speed and agility. Oddly, they were only used in one episode (where they handle the Avatar) and are never seen again. One of them shows up as a member of the "Rough Rhinos" that reappears a few times in the series. However, he was actually booted out of the Yu-Yan for failing a critical mission. The General from "The Blue Spirit" implies that the Yu Yan archers are used only for certain tasks.
The Equalists from The Legend of Korra appear to consist purely of these. A few trainees and hangers-on have gone down easily enough, but every single uniformed member of the group has been able to give the main characters a good fight. In their first appearance they actually beat the heroes in even odds!
In Book 2, the Dark Spirits are eventually revealed to be this, working for Vaatu and therefore for Unalaq, who uses them as secondary troops when his waterbending human soldiers are defeated.
Regular Neosapien mooks in Exo Squad were gradually reinforced with more powerful Neo Warriors and Neo Lords in the second season. Not that any of them had a real chance to harm a recurring character...
Season 3 of Generator Rex features the "Black Pawns," elite soldiers brought in by Black Knight after she takes over Providence. They wear all-black versions of the standard Providence uniform, and are far more skilled at hand-to-hand combat than regular mooks, even giving Six a run for his money. Later episodes imply that they're now the field commanders for Providence operations, even getting their own custom vehicles.
Cobra Commander has his Crimson Guards, who were supposed to be of significantly higher quality than Cobra's basic blue-shirt mooks, but who (at least in the '80s cartoon version) generally proved as ineffective against G.I. Joe's named character squads as the lesser mooks. At least one or two Crimson Guardsmen got a minor Crowning Moment of Awesome (i.e. the one who fights his way out of a top secret lab in one episode), but would usually screw it up at the last moment with a cringeworthy mistake (the aforementioned Crimson Guard accidentally dropped the chemical he was stealing, creating a giant amoeba that ate him and half the county he was in... Cobra's experiments had a funny way of unexpectedly doing wacky stuff like that.)
The toyline also had the Crimson Guard Immortals, the elite of the Crimson Guard. Possibly a Shoutout to the Persian Immortals.
The Fourth Mask shadowkhan from Jackie Chan Adventures could be considered Elite, as they nearly had super-strength and were almost impossible to beat without the strength talisman, or similar.
During one episode of Kim PossibleDr. Drakken discovers how worthless his Mooks are so he sends Shego to steal strength-enhancing rings that transforms the wearer into peak condition. They didn't become any better so they were defeated quite easily by Kim (and still proved to be much more reliable than the Elite Mooks by herself...).
Star Wars: The Clone Wars introduced the BX-series Commando Droids, the Elite Mook version of the standard Battle Droids. They had enhanced armor, nearly General Grevious-level agility, and a number of neat tricks such as magnetized feet to resist Force pushes. They were a decent threat to clones, but still no match for the Jedi (although they were at least able to put up some resistance).
The Monarch briefly employed Black Guards, who appear much more menacing than his regular henchmen (but Subverted as the Black Guards all used to be regular henchmen; even typical non-action villainess Dr. Girlfriend handles several in a fight without issue), as seen in the page image.
Also the "Strangers", the team of soldiers used by the Guild, all appear to be Elite Mooks. Brock even seemed to be wary of them the first time they were shown. They have been seen freezing a room of people solid and then administering memory wipes in the event that somebody is about to give away a crucial piece of information.
In Teenage Mutant Ninja Turtles 2003, the Foot Clan has Elite Foot Ninjas (the guys in the red robes and coolie hats). Unlike many Elite Mooks, these guys actually were demonstrably better than the standard cannon fodder Mooks, able to fight evenly against the turtles and almost killing them in their first appearance. A big contributor to the Foot Elite always posing a threat would be that there's only four of them.
After realizing that his regular mooks just weren't cutting it, Teen Titans Season Three Big Bad, Brother Blood, replaced them with completely mechanical copies of Titans member Cyborg. The Titans still managed to take them down, but it took a lot of strategizing and improvising where ordinary mooks would have just been effortlessly blasted through.
The Insecticons are massive, vicious, bestial Decepticons vastly superior to the general Vehicon troops. One on one, they can give even the strongest of the main cast a run for their money. Fortunately for the Autobots, they go down much more easily in groups than as individuals. And even then, when they're at larger numbers, they're usually in their more vulnerable beetle-like forms (which canonically have lighter armour). Insecticons in this series are subject to Conservation of Ninjutsu, but not to the same jarring degree as most mook squads. When they're at their most dangerous, they tend to fight in smaller squads and provide relatively tough opposition to the Autobots.
The Predacon army that Shockwave was cloning would have likely made the Insecticons look like houseflies by comparison, if the few that eventually surfaced are anything to go by. However, after seeing how fully the first specimen exceeded expectations, Megatron pulled the plug on the project out of fear they'd eventually wind up threatening the Decepticons as well. This information got out at exactly the wrong time.