This can happen every couple of books early on in the series Lone Wolf. Of course, you're still a psionicBadass. Notably: in Book 2, after you get shipwrecked; in Book 5, 9 and 17, if Lone Wolf has to get out of jail; and unavoidably in Book 7, Castle Death, when thrown into The Maze.
The whole book 4 of the GrailQuest series, Voyage of Terror, is this trope. The hero Pip is accidentally sent to ancient Greece instead of Avalon, and starts out with none of the usual equipment, nor the numerous magical items that could have been gathered during the 3 precedent books, including Excalibur Junior. Sure, you can find some new weapons, armors and magic along the way, but none of the usual fare until the next book.
Dungeons & Dragons adventures A3 and A4. At the end of A3 Aerie of the Slave Lords, the characters are captured by the title opponents: they have no chance to avoid it. At the beginning of A4 In the Dungeons of the Slave Lords, they wake up in the title location with no weapons, though they can improvise some from their belongings.
One Pathfinder module has the party trying to retrieve an item from a shop in a section of a marketplace where weapons aren't allowed (except for the shops' guards) and magic is suppressed, and the shopkeeper doesn't want to sell it. (Judging by the Dungeon Master notes, the expected method of obtaining it is to use items in the shop as improvised weapons.)
Video Game examples
In The Legend of Zelda: The Wind Waker, Link arrives at the Forsaken Fortress via cannon and loses his sword in transit, requiring the use of stealth until the sword is recovered.
In Oracle of Ages, your equipment is stolen about a third of the way through the game when you are stranded on an island.
In A Link to the Past, to get the Tempered Sword Link has to hand his weapon to the smith brothers and wait until they're done. He can still attack enemies by ramming into them.
Twilight Princess has segments where Link become a wolf, rendering him unable to use weapons or items (the first time even involves you being captured and imprisoned). However, you can still fight about as well as you could in human form.
The third trip to Eldin Volcano in The Legend of Zelda: Skyward Sword, you even have to run around collecting all your gear. Thankfully, you're given your Mogma Mitts for free - you can't get anywhere without those, as you're trapped in a cell.
Also in Skyward Sword The Silent Realms qualify as this as well.
Every Tomb Raider game does this at some point or other, to varying degrees (in some you lose your weapons but keep ammo and other items, in others you lose just about everything, and in a select few, you play a level or two where weaponry is simply not available).
The Last Revelation and Legend have flashback levels where you play as a younger Lara where she doesn't carry weapons. These levels are focused on puzzles and platforming with enemies you have to avoid or find a way to disable them.
It's worth noting that in the third game, where you lose almost everything, med kits included, said loss is permanent. In addition, the player decides what order to complete the middle three of the five areas in, and if you pick a certain area last... Well, sucks to be you. It doesn't help that said area is listed as the last of the three in most official material.
The final chapter in Tomb Raider Chronicles has one level where Lara must give up her weapon by placing it on a tray because the hallway nearby is a security scanner. Trying to go through it with a weapon will trigger some turrets and kill you quickly. Until you can disable the security scanner, Lara can either use chloroform to knock out guards or just avoid being spotted.
Metroid: Other M has one at the end of the playable epilogue where Samus takes off her suit (and thus, all her gear) after she gets what she is looking for, only to get interrupted by a count down sequence. Samus chooses to escape in her unarmored state using nothing but the stun pistol.
The Ratchet & Clank series often avoids stripping Ratchet of his weapons (even when kidnapped and imprisoned in Going Commando, he keeps all of his weapons. However, there are still sections in which Ratchet is incapable of using Clank and his abilities, therefore relying on much more precise platforming, and arena levels which restrict Ratchet to one gun, or even just his wrench.
In fact, if Clank is considered 'gear', then the levels in which he's without Ratchet can be considered an inversion of this trope.
Ratchet & Clank: Size Matters features Ratchet kidnapped and sedated, playing through a trippy dream level. When he wakes up, he finds himself stripped of his guns and must use his wrench and the guns of his that he finds strewn on the ground as he makes his way out. Eventually, he'll find the entire rest of his arsenal stowed away. Frustratingly, the game does not keep track of the way your quick select was organized before the level, and you'll have to reorder your inventory every single time you play this level.
Little Big Adventure features a jail which strips you of your items, conveniently stored nearby once you disable the guard who comes into your cell, naively.
During the final boss fight in Ōkami, all of your brush powers, the ones that you spent the whole game acquiring, are stripped away. In order to get them back, you must damage the boss the old-fashioned way — pummeling the crap out of it with melee attacks until you get them all back.
Also occurs during normal gameplay if you are careless enough to run out of ink — your weapon vanishes as well, leaving you to fight with tooth and claw. Horrible during boss fights. Luckily, ink replenishes.
In Prince of Persia: The Sands of Time, near the end of the game, Farah steals both your sword and the Dagger of Time to go complete the mission on her own. Thankfully, you get a ridiculously powerful replacement sword a few minutes later, but not before you have to run for your life from some hulking monsters. Unfortunately, it takes longer to get the Dagger back, meaning you have to be very careful as you inch along hundred-feet high scaffolds.
This actually happens twice in Prince of Persia: Warrior Within. Near the beginning the Prince's ship crashes and he loses his sword. Once washed ashore, he has to do with a piece of driftwood and whatever secondary weapon he managed to grab off the enemies (amusingly, those weapons break with use, while piece of wood doesn't.) Then after the Disc One Final Boss, Dahaka breaks his primary sword again. And the next sequence of levels involves eventually finding a new one. Said broken sword does absolutely no damage so you're stuck using grab moves and whatever secondary weapons you can scrounge up. Probably most problematic is that you're not likely to notice that your sword is broken until you actually get into a fight and realize your sword isn't what it used to be...
The whole thing is lampshaded in Prince of Persia: The Two Thrones, where the Prince laments, "Why is it that every time disaster strikes, I find myself without a proper blade?" (This reference goes all the way back to the original Prince of Persia, where you start out unarmed.) Following that, you get a tutorial about Quick Time Event stealth-kills with a random knife he picks up.
On your way to finally put down Gary in Bully, you're met at the doors of the school and rather rudely stripped of ALL weapons. Including the infinite-ammo rubber-band ball and the infinite-ammo slingshot. It's Good Old Fisticuffs to finish your grudge.
In Prototype, you lose access to all your selectable powers except for disguise for two whole chapters. Particularly annoying as it's an open world game, and you don't gain them back between chapters, limiting the number of side-missions you can do successfully at that time.
Psygnosis' O.D.T: Escape Or Die Trying has a level where you exit a prison and get jumped by four wardens. Then you find yourself not only without items, but also without spells.
Kya Dark Lineage: After Brazul captures and imprisons you, you lose all your equipment and have to retrieve it. It's really difficult not being able to fight Wolfens or use your Boomy.
The most annoying levels in Castlevania: Lords of Shadow feature the Chupacabra, a misnamed gnome-like thing that steals all your relics and magical items. You keep your fighting combos, but lose other skills like double-jump and dash, and you have no way to heal. When you catch up with the little runt he'll surrender your stuff, but sometimes there's a Cave Troll in between...
Star Fox Adventures has Fox get imprisoned and his magic staff (the only piece of equipment he has, but which contains the staff powers he has gained thus far) taken off him in one stage. The stage thus revolves around sneaking around the prison to get the power needed to get it back by fooling the guard into thinking you're his replacement, so he'll leave.
The SNES version of the movie Judge Dredd has you stripped of all weapons before stage 3, save for the pistol. All you have is the Lawgiver the entire game. You just lose the rest of your Abnormal Ammo.
Alien vs. Predator 2 has two of those (disarming an alien is somewhat... difficult). For the marine, it happens pretty early in the game and is a rather standard scenario. You are helped by the fact that a fellow prisoner hands you a knife (well, you grab it off his barely-cold body...) and the first enemy soldier posthumously donates you a pistol about six seconds after the mission starts. The predator is trapped, shot unconscious and shipped off to the human base for research. For obvious reasons, the scientists try to disarm their prisoners, but hesitate when taking off the arm blades of the first one induces cardiac arrest in the specimen. The predators do not like being without a weapon...
Harry The Handsome Executive makes this slightly more bearable than some other examples — the same challenges that cost you your weapons gain you magical powers.
The final boss in Viewtiful Joe 2 strips Joe and Silvia of their movie superhero powers. All the abilities you've bought and learned are gone. However, after a short pre-fight using their weaker forms, the spectators use Clap Your Hands If You Believe to revitalize the duo.
Metal Gear Rising: Revengeance has an interesting variation: Raiden still has all his gear, but he's so emotionally distraught he can barely control his cyborg body properly, making him slow, clumsy, and helpless if ganged up on, forcing you to sneak around enemies for a bit.
A variation exists in The Wonderful 101: During one level, you have all the skills and items you've acquired over the game, but you start the level with just ten Wonderful Ones in your party, with almost no ability to bolster these numbers until later in the level. For reference, when you first open a new save file, you start the game with twenty. This makes it extremely difficult to make use of Unite Morphs since a single hit scatters your forces every which way until you gather them up again. As a result, even weak enemies that were obsolete from the second level are suddenly challenging again since your attack power is weak and your evasive options are often locked due to a lack of Wonderful Ones.
KOTOR 2 has this happen fairly early on, and you only have two fights sans-equipment before you get it back.
Deus Ex, which makes the Warren Spector quote ironic as he was lead developer on the game. However, unlike many other games, you are immediately re-armed with a lot of good weapons and tools the moment you escape, making this much less of a pain, unless you rely too much on Assault Rifles or Shotguns.
Also due to the fact that ammo has no mass or volume in Deus Ex, despite taking away the player's heavily modified and upgraded rocket launcher, the bad guys were kind enough to leave JC the stack of twenty rockets sticking out of his pockets, meaning that more than likely the instant you FIND a weapon you'll have enough ammo to liberate several more.
One nasty stumbling block is that if, when you finally reach the armoury that contains your own heavily-modded equipment, you have a standard weapon (such as one recovered from one of the guards) equipped, then picking up your modded item of the same type destroys that weapon, recovering only the ammo it was loaded with. If you've collected unmodded replacements for all your original weapons by the time you reach the armoury, it's entirely possible to do this to all your original gear, never even realising that it was your upgraded items in there at all, and have to start from scratch re-upgrading your items.
It can also be circumvented entirely - just quickly press the menu button, drop your gear and re-equip it, then tear through there with great ease.
"The Missing Link", a DLC chapter for Deus Ex: Human Revolution, takes Adam's gear and disables his augmentations at the start. You retain your basic abilities, including Adam's One-Hit KO takedowns, but you don't get your original gear back, since the chapter is stand-alone from the rest of the game.
The Director's Cut plays this completely straight: for the entirety of The Missing Link, you are depowered, lose all of your gear, and keep only your money, forcing you to make do with what you can grab. At the end of the chapter, just before returning to the main story, you are given the opportunity to grab all of your original gear, and get enough praxis points (combined with any you earned during the chapter) to bring you back up to your original level of ability. It also allows you to essentially respec, since you get the points, not your original abilities you had before.
Late in Kingdom Hearts, Sora loses the Keyblade and must fight through Hollow Bastion using only a toy wooden sword. This is eased, however, by having the Beast fighting alongside him. You can cast spells too, but that might not help so much if you're one of those who specialized in combat and since the Keyblade also enhances your magic, that ends up weakened as well.
Happens again in 358/2 Days. Xion can't remember how to summon her keyblade, so you give her yours for a mission. What do you use? A stick.
Happens in Fable, as well. Your character ends up in a prison cell with nothing but his undies. Thankfully, you get your equipment back about ten minutes later.
And again in the sequel, though it's a bit more complicated the second time around.
Avalon Code has a particularly vicious form of this. The protagonist is a kid who's rather pathetic at combat but happens to come across the BookofProphecy and becomes insanely proficient with any weapon that is literally pulled from within it. Then Chapter 5 ends after the Big Bad tricks a character into stealing the Book from you and attempting to use it himself, and another villain steals it in the aftermath — on top of an All of the Other Reindeer moment that neighbors Phantom Brave proportions and you're back to being a puny kid. Heath decides to fix that and teach you to fight without weapons — which you have no choice but to do for the entirety of Chapter 6.
Though it does help that after only two training sessions with Heath the puny kid is suddenly able to fire massive energy blasts out of his/her fists.
In Revenant, there is absolutely no indication that you should be leveling your "Hand Combat" skill, until you are stripped naked and set to fight the Ogrok Hand Combat champion.
In Ys IV: The Dawn of Ys, you start out with the Cleria equipment from I and II, but you are stripped of it and thrown in the dungeon shortly after.
Happens in Drakensang 2 at one point during the story. You can only count on stinky fish and eventually the weapons you can take from the guards.
The Elder Scrolls Adventures: Redguard has this when you are thrown into the catacombs.
Mass Effect: Subverted. When you first reach Noveria in the first game the local security guards want to strip you of your weapons before you enter Port Hanshan. Just before you hand the guns over (or gun the security guards down) a voice over the intercom tells the guards to stop harassing you and let you pass.
One of the DLC chapters in the second game plays it straight after the main character is captured. It only takes about a minute to get all your gear back though.
Kasumi's loyalty mission also forces the player to solve a few puzzles and deal with a few weak enemies whilst equipped with only a pistol. Again, your weapons and armor are soon returned.
The segment near the end of the second game where you play as Joker can count as this, as he's on a stealth mission with no equipment and can die easily.
Although by then there aren't very many enemies left to fight, the last leg of the final game's final dungeon has Shepard going it alone, no armor, and only a pistol. All other weapons are presumably destroyed or lost when Shepard is caught in an explosion prior to reaching the ship, which also reduces their armor to a charred mostly destroyed undershirt.
Rune was billed as a game where manly vikings, yetis, dwarves, and giant zombies chop each other to pieces with swords so huge they don't even fit on the screen. While most of the game easily lives up to this, your character is killed in a cutscene right after the tutorial, and then brought back to life in a dank underwater cavern with no weapons. You only get to do anything interesting after working your way through Underwater Ruins full of goblins, crabs, jellyfish and malignant sea anemones.
The "No One Escapes Cidhna Mine" sidequest, which strips you of all your inventory items (though magic is still available, you're given a pickaxe, and you can bargain with your fellow inmates for a shiv). Your stuff is all given back to you at the very end however.
Weirdly averted in the main quest when you must infiltrate the Thalmor embassy. A collaborator can smuggle some equipment in for you, and instructs you to bring only what is absolutely necessary, but there's no weight limit on what he smuggles in, so you can dump your entire inventory on him and pick it up again ten minutes later without ever having to get into a fight.
In Tales of Monkey Island episode 1, at one point you're strapped to a table and can't access your inventory, and are extremely limited in what you can interact with.
In Simon the Sorcerer 1 you lose all your inventory after getting shrunk. You won't get it back, but you no longer need it, anyway.
Jak X has a late-game level where your vehicle has been sabotaged so you can't use any weapons, forcing you to rely on turbo boosts and pure driving skill alone to get a decent position. The bigger problem is moreso that the weapon mechanics in this game revolve around allowing you to block opponents' weapons with your own, so not being able to use any pretty much makes you a sitting duck.
Golden Eye 1997 for Nintendo 64. In fact, this happens twice. And both of them are Escort Missions. In the first one, you have the option of leaving Natalya in her cell until you've cleared out the rest of the base.
In Agent Under Fire, you can actually prevent this from happening, if you find a keycard before you enter the submarine in the Poseidon level.
XIII: In a particularly creepy instance of the trope, you must escape from an insane asylum.
Subverted in Star Wars: Jedi Knight II: Jedi Outcast; you have your main weapons confiscated upon entering a bar in one level, but are otherwise unrestricted and get to keep your lightsaber. Since it's the first level where you have the saber, it could be seen as a way of forcing the player to start relying on the saber rather than guns.
Played with in the sequel, Jedi Academy: there is a level in which the player is captured and stripped of all weapons and then has to escape. Gathering weapons is not difficult, as there are plenty lying around, but the player is denied one of the most powerful weapons in the game — the lightsaber. This is deliberate on the part of Jaden's captor, who's created a blood sport out of letting dangerous prisoners try to escape while he hunts them down. Of course, he's never hunted a Jedi before, and doesn't consider finding a way to take away the other most powerful set of weapons in the game: Jaden's force powers. One of the simplest and most cathartic strategies when you face the guy is to Force Push the shots of his concussion rifle right back into his face.
Also in predecessor Dark Forces — Kyle Katarn gets captured by Jabba the Hutt's henchmen and dropped into a pit with at least one kell dragon. Fortunately, he can dodge its attacks and kill it with enough hits from his fists.
Though it is possible to recover your lightsaber by Force Pulling it while standing in the right place.
Additionally, in the last level none of your weapons except for your lightsaber even work.
Happens fairly early in Tron 2.0. Particularly irritating in that one of the weapons you lose costs energy to acquire in the first place — energy which might have been better spent elsewhere — and upon losing it you cannot retrieve it (you do eventually get your frisbee back, though, and are also given a new weapon to make up for it). And there are several infinite (and, until you leave the level, infinitely reusable) energy sources between the time you acquire the weapon and the time you are relieved of it.
One of the levels later in Perfect Dark has you held prisoner on an alien starship. After waking up, you realize that the only weapons you have are a throwing knife and your fists. Strangely enough, this is one of two levels that not only doesn't require, but doesn't allow, some degree of stealth. It's not much of a hassle to collect another weapon though, since you can disarm the aliens and take their blaster pistol. Be careful, though: Using all of your ammunition before destroying the computer terminals immediately fails the mission.
Earlier on, you must sneak into an air base to infiltrate Air Force One, and on higher difficulties, one of the objectives forces you to drop off all your weapons at the baggage check so you can get through security without your disguise being compromised. It doesn't become a problem until you deactivate the security system so they're not detected, because that's when the NSA agents decide to spring their plan and shoot up the place.
The virtual deathmatch in Perfect Dark Zero starts you off with only a MagSec4 pistol, while Mai Hem is armed with a Superdragon assault rifle. Fortunately, if you activated the sattelite dish earlier, Chandra can hack the game and send you an M-60 machine gun.
In Doom 3, shortly after deciding whether to call the fleet or not, the PC's teleported to hell and loses all his weapons. Then you're fighting the big monsters you've been saving rocket shells for with a shotgun and dead ends.
Back in Doom 1, the game was divided into episodes. Starting a new episode meant starting with a pistol again. Also, in Doom 1 and Doom 2, if you die, you can restart the current level with 100 health and a pistol.
The Doom 2 mod Vanguard has the player to die at the end of level 5, forcing him to go through level 6 (aptly named "Punchline") with nothing but a pistol and a berserk fist. All these imps and zombiemen suddenly become a real threat, and the moment where you get the shotgun back gives you the "yeah, I'm back in the game!" feeling.
Also inverted in Half-Life 2: Episode 1, in that it happens early in the game before you have much of a weapon collection, and the gravity gun is immediately turbo-charged to use for more gameplay goodness than HL2 allowed with it.
Duke Nukem 3D, captured by Pig Cops. After the second level. And if one isn't paying attention, they'll die instantly at the start of the next level: the pigs are going to electrocute Duke via electric chair!
Command and Conquer: Renegade, captured by stealth soldiers. However in this case you never get back the weapons taken from you, and have to rebuild your arsenal from almost scratch, save your pistol. Also interestingly, as soon as you rescue any given prisoner, they automatically get a gatling gun from seemingly nowhere. You never recover your reliable, accurate assault rifle either. Sniff.
Possibly because the chaingun is (oddly) just as accurate, and you have better weapons to use down the line like the laser rifle which is also accurate
This occurs in Postal 2, when not only are you knocked out and kidnapped, but you wake up dressed in a Gimp suit. After escaping and getting your weapons back, you then have to go to the laundromat to change back to your regular clothes.
An optional version in the police department, if you gain notoriety with the police and allow them to arrest you. They take away everything except for your box of matches. Like above, it's possible to regain everything you had beforehand.
Happens three times in Red Faction. In both cases, you are able to rebuild your arsenal the same way you built it in the first place (taking guns off dead enemies), but whatever weapons and ammo you had originally are lost. On the plus side, one of these sequences can be skipped — just ignore Hendrix's insistence that you need a disguise in the hospital.
Far Cry uses the trope in an uncommonly logical manner: You actually start the game unarmed after a shipwreck, and spend the first level seeking out weapons. A more typical example occurs later, toward the end, when you lose everything after getting captured.
Far Cry: Instincts does this three times, though logically; the first time, you're crawling out of a shipwreck with only your switchblade, while the second time you've been captured, and the third time you've just woken up from surgery to find you've beaten fifty men to death with your bare hands and all hell has broken loose.
Far Cry 2 has essentially no connection to the previous game, but in one level you and your main buddy are captured and taken to a prison. Oddly enough they leave your machete on you but take your guns, but there's very little fighting in the prison itself; it's a short run straight out of the cells past no guards to get outside, and from there you can sneak up on a hut on the road and steal some supplies. As soon as you get out of the prison you're able to get to a gun dealer and totally restock.
Also happens in Far Cry 3, when you get captured (twice). The first time, you find a basic gun pretty quickly, and it's all you need to escape. The second time, you still have your machete, and are able to kill a guard quickly to get his gun (not that it's terribly useful, since stealth rules the day and the gun is unsilenced). In both cases, as soon as you're done, you can go back to a weapons dealer and restock: the weapons are not themselves unique.
Some of the mods for Wolfenstein 3D had individual levels where you started off without weapons.
Return to Castle Wolfenstein begins this way. The Xbox version added an extra chapter before the opening, which makes it more of this trope when you're thrown in prison without your weapons.
In The Conduit, you can finish a level armed to the max with your favorite weapons — including rare super-weapons with One-Hit Kill capability — and then lose them all when you transition to the next level.
BioShock has Fontaine Fisheries, where Peach Wilkins won't let you advance unless you turn over all your weapons. You fight through the freezer area using only plasmids and a wrench, though you can find one or two dropped guns. That said, it is possible and in fact quite easy to cheat and bring a weapon in with you, as the gate which opens when you surrender your guns doesn't close again if you pick up another one and it's possible to carry items around with the telekinesis plasmid without collecting them.
Just to twist the knife, almost all of your meticulously saved ammo is "missing" when you do recover your weapons.
This happens three-fifths of the way through Resistance 3, after Joseph Capelli is captured by the Wardens. Interestingly, you start with getting two new weapons before you ever recover the old ones: The Sledgehammer and the Mutator, and the returning weapons you do get at first are the rather low-tech ones; the Carbine and the Magnum, for example. The most interesting part, however, is that you don't actually end up recovering all of your weapons by the end of the level, and you'll arrive at the next only to check your quick select and realize that they still aren't there. Fortunately, you recover them fairly quickly after this.
Turning Point: Fall of Liberty strips you of your guns and ammo at the end of each level and replaces them with 1 or 2 preset guns (often not very good).
Call of Duty: Modern Warfare 2 has one of the most intense levels of the game, when Soap, Ghost, and Roach fight their way through a Favela. Near the end of the level, your squad requires you evacuate. Cue running across rooftops. Of course, you miss a gap, fall off a ledge, and black out. You don't have time to reclaim your weapons, so you run half a mile through a massive slum to get back to the rooftops without the weapons you were kicking ass with earlier, with an entire militia on your tail, and make a breakneck jump to "get to the chopper", with a final leap that pays homage to the original daring escape made by Soap in Call of Duty 4 on the cargo rig.
The first Modern Warfare has "Hunted", where the player's chopper gets shot down on the way back from the "Blackout" level and you start out with only a pistol. There are more weapons lying around the crash site, however, but they're just regular assault rifles and SMGs, rather than the extensively-modified gear you had for the previous level.
Serious Sam does this constantly. In The First Encounter, it was actually a variation of it where, at the end of one level, most of your ammo is taken away but weapons still remain. In The Second Encounter and Serious Sam II, Sam loses weapons after every chapter due to teleportation restrictions. In the last chapter of Serious Sam II, you'll lose your weapons by being captured.
This is a severe punishment in Bloodwings: Pumpkinhead's Revenge, for apparently if you take anything from a certain cutscene that was not actually a scene from the movie, a group of children will warn you to put it back. If you choose to deny their demand, they strip you of your entire inventory, thus pretty much rendering the game Unwinnable.
One of the "Roll The Dice" results leaves you with only the use of your Melee weapons and nothing else. A slap on the wrist if you're next to your spawn, a death sentence for any spy behind enemy lines now left with only his knife (but no disguise kit or cloak watch).
In F.E.A.R., several psychic vision sequences in the final Interval inexplicably make all of Point Man's weapons vanish and equip him with a pistol.
F.E.A.R. 2: Project Origin strips Becket of his gear after the first level, as he is critically injured by the nuclear explosion (from the first game) and taken to Armacham's hospital where he later wakes up.
In F.E.A.R. 3, Point Man manages to lose his entire inventory at the beginning of every single level. In the later levels he at least starts out armed, but often only with a basic pistol and submachine gun at most. An attempt is made to justify this by having nearly every level begin with Point Man recovering from some destructive event, such as a helicopter crash, a flood, falling off a bridge, etc, in which he'd naturally lose much of his gear.
In Si N, John Blade is mutated into a monster right after one of the later stages, and spends a whole level (plus an optional bonus one) running through dangerous and deadly test chambers before being turned back into a human, which immediately reverts him back to his human form - along with all his weapons, ammo and special items returning (with no explanation of where they were in the interim).
In the middle level of Allied Assault's "Behind Enemy Lines" mission, you start with only a silenced pistol, and have to infiltrate a tank encampment by stowing away on an enemy truck (unless you prefer the hard way). Luckily, there's a Kar 98 sniper rifle just after this part, and plenty of SMG's and ammo.
Dishonored has a brief one of these. After the Loyalists turn on you and poison you, you are left for dead in a prison cell with all of your gear thrown to the bottom of a shaft. You can make your way back to this shaft to recover everything if you so choose. It will also net you the achievement/trophy "This is mine".
Played straight and subverted in Aliens: Colonial Marines. One level has Winter being captured and cocooned (but escaping before being facehugged), and losing all his weapons in the process. However, O'Neal somehow managed to save all of Winter's equipment in a duffle bag, and gives it back to him near the end of the level. Later on, after the Marine dropship crashs and destroy everything onboard, the player retains all their weapons, but they don't make a dent in the xenomorph queen (necessitating the usage of a cargo drop mechanism to push her out of a ship).
Massively Multiplayer Online RPG
This is essentially the entire purpose of the Exemplar/Malefactor (Cross-level team) and Flashback (repeating a quest) features in City of Heroes and City of Villains. The game doesn't make extensive use of in-game items, but you receive an effective level reduction, losing access to any abilities and enhancements you achieved after the level you've been reduced to.
The idea behind the Kung Fu Hustler skill in Kingdom of Loathing is to turn the character with it into a Bare-Fisted Monk: if you have it and don't have any weapons equipped, you get four intrinsic effects that boost your power by a considerable amount. If you equip weapons (or off-hand items which aren't weapons), you lose the effects at the start of your next combat.
Also used in one of the game's Self-Imposed Challenge paths, "Way of the Surprising Fist", which gives you the opportunity to learn some powerful martial-arts moves but prevents you from using weapons or off-hand items. In fact, you can get a trophy for acquiring both Kung Fu Hustler and Master of the Surprising Fist as permanent skills.
Salvage in Final Fantasy XI strips players of the ability to use all gear upon entering (the excuse is something about psychowaves in the ruins). Special cells dropped by enemies can be used to lift the equipment restrictions, slot by slot.
In The Secret World you can't just have your gear taken from you; stuff made for you will respawn in your possession the way you yourself do. But there are ways to disable most of your supernatural abilities within an area, rendering it all inaccessible. This is one of the ways the game (which has no explicit stealth powers) implements a Stealth-Based Mission.
There's even one mission which requires combat without gear. Fortunately, it turns out that among the many hidden triggers implanted in your mind (usually used to explain your differing abilities in cutscenes) includes one for this which loads up a set of boxing- and jujitsu- based skills, backed by the slight physical augmentation you still possess... and the Big Bad of the arc was smart enough to disarm his normally lethally-equipped security force (the point is to keep you locked down; kill you and you could respawn anywhere). The whole thing naturally culminates in a Fisticuffs Boss.
In Zone of the Enders you have to play a mission as a damaged mook Raptor with a limited repertoire.
The parts in Super Mario Sunshine where you lose FLUDD. The FLUDD is a water device that lets Mario spray enemies to stun them or allow Mario to hover and clear gaps. When you don't have the item, you have to rely on precise jumping to get to each platform and have to use other moves to stomp enemies.
Both versions of the Final Caves and in the Sacred Grounds levels of Cave Story. 'You feel a black wind pass through you. All levels dropped to level 1!"
Happens twice in Heart of Darkness (an adventure game somehow similar to the first Oddworld): when you start the game you have the electric equivalent of a flamethrower with which you zap hordes (literally) of shadowy monsters. But of course, you lose that weapon before the end of the first level, so, since you're playing a twelve years old with no other means of defense, you have to run helplessly for the rest of the level. However, later in the game, you find a magical rock that grant you powers, and you can start zapping monsters again... until later on when the rock is destroyed and you lose your power... only to find back your electric weapon a moment later.
In Kirby's Return to Dream Land, when Kirby enters the other dimension through the openings unlocked from using the Ultra Copy Abilities, he loses his ability and must make his way through an obstacle course with only his normal moves.
Real Time Strategy
Warcraft III: the Blood Elf campaign has a level where you start with just Kael and Vash, freeing your imprisoned elf soldiers. Most are actually locked up without arms or armor (and use the civilian elf models to reflects this), but as soon as they're rescued run over to a rack to regain their weapons, armor, and magic powers.
In a rare unscripted version, NetHack has nymphs, who seduce your character, steal your equipment and then teleport away. More than a few players have died because they were suddenly left weaponless after running into a nymph. (Of course, this is NetHack. More than a few players have died falling down stairs. Everything Trying to Kill You is a bit of an understatement.)
ADOM twists this by making the player voluntarily give up his equipment. Just hanging inside the Tower of Eternal Flames, fire immunity or no, will randomly and permanently destroy things from your inventory (with fireproof blankets/rings of ice as a partial countermeasure). Falling down the Rift breaks a good portion of your currently carried inventory and the only way to diminish the effect is to have the few good/not too awful corruption effects among an array of nasty ones. On both occasions the smart player is forced to stash most of their rarer belongings somewhere and having to get by with only the bare essentials. Using artifact weapons/armor is an option due to their indestructible nature, but they also accelerate the player's food consumption, making starvation a real possibility.
In Final Fantasy Fables: Chocobo's Dungeon, all of the special dungeons prevent you from bringing in items including gear from outside; upon entering, your inventory is put into your storage (if there isn't enough room in storage, you can't enter). Upon leaving the dungeon you get to keep everything you found inside and can go to storage to retrieve your former gear as well.
In Final Fantasy XII, you're thrown in jail at one point and stripped of your equipment, but still get to keep all the spells and techniques you've acquired so far.
Averted strangely in Final Fantasy V, where your party is sent to jail, but allowed to keep all their weapons and items. Going even further, they're in a cell right next to Cid, who was apparently allowed to keep enough explosives to blow a hole through the wall. The game contains a later instance where this trope is played straight.
Similarly, in Final Fantasy X, your characters are tossed into a dungeon after being arrested and yet still have all of their weapons and equipment.
In Final Fantasy VIII your characters are captured and thrown in prison with all their weapons taken from them. Not really a problem since one of your characters doesn't use weapons. So it's up to him to go alone through the prison to find the weapons (conveniently left in a pile where he can get them easily).
Also in Final Fantasy VIII inflicts this trope on the player as well. When you enter the final boss's castle, all your combat-menu commands are sealed off, with the exception of standard physical attacks. To regain use of them in the castle, the heroes must win several lesser boss battles, with each victory unlocking a combat command of the player's choice.
A stat variation in Final Fantasy VIII, the fourth form of the final boss can "blow" away the party's junctions, effectively lowering stats to miniscule amounts.
In Final Fantasy VII, Yuffie steals all of your materia once you start the Wutai sidequest. (If you have a LOT of materia, she'll actually leave a few, but you're not likely to have enough at the point when the sidequest first opens unless you spent a lot of time grinding.) This is extremely devastating since materia not only gives you your abilities, but it also alters your stats. Without materia, your party is severely gimped, even with the best weapons and armor. To rub the salt in the wound, any materia you find during the side quest is immediately stolen by Yuffie on the spot.
Granted, if you delay it for a brief while, the Temple of the Ancients holds numerous weapons that lack materia slots but have higher than normal base stats, presumably to help compensate for the theft.
Chrono Trigger has one of these, along with an earlier imprisonment that for some reason didn't dequip you. In the later case, you indeed lose all your weapons (and all other items) and have to avoid the guards until you get them back, since your characters can't even defend themselves without a weapon equipped. Apparently, you can't cast magic or use tonics without a sword or gun. On the other hand, if your active party includes the Badass Normal cavewoman who laughs at such silly ideas as weapons, she can go to town on them from the get-go.
This can appear in dungeon adventure games as well. In some of the harder levels of Pokémon Mystery Dungeon, you are not only stripped of your current items, but also reduced to Level 1. Ouch.
In Breath of Fire: Dragon Quarter, going into the Bonus Dungeon sets your level to one (temporarily, thankfully); it doesn't take your equipment, though, and it can be circumvented with Party XP, which can be applied at will (and isn't restricted in said bonus dungeon).
Early in Tales of Phantasia, you are stripped of your weapons and tossed in jail, but quickly (and morbidly) retrieve a replacement Long Sword from the body of another prisoner who helps you escape with her last breath. You probably just replaced your starting Long Sword, so it's not too bad... but woe to the gamer too clever for his own good who got the very nice Knight's Saber before triggering the jail scene.
In Ultima VII Part II: Serpent Isle, you are stripped of all your weapons early on by uncontrolled teleportation magic, but quickly scrape up at least serviceable weaponry. Later on, you are thrown into prison for a crime you may or may not have chosen to actually commit and stripped of all your weapons — only to discover that THIS is where the previous game's Infinity+1 Sword was teleported at the start! The weapon retains all its previous power. Your windfall doesn't last you long, though: To escape the prison, you must destroy the gem in your sword, rendering it powerless — with the demon contained within killing the Big Bad of the prison in a rather gory fashion, letting you escape. You still get some other loot in this sequence, meaning that when you get your existing equipment back you end up the richer for having been imprisoned.
In the Expansion Pack for this game there are more of this: Three trials that make you fight some enemies, avoid traps and such, all alone and without any of your equipment. Every time you end one of the challenges, you'll end with better and better equipment. The kicker: The ones who sent you to the trials were your ENEMIES, they were in fact trying to get you killed, and they only managed to make you stronger, richer, and better armed for the next adventures. With enemies like those...
Played straight in Ultima IX, which sends the Avatar into Deceit with no weapons or spells at all. Not only do you have to escape the dungeon without them, you have to complete the island's adventures before your equipment is recovered.
Neverwinter Nights: Hordes of the Underdark does this at the beginning of the expansion. Not terribly annoying if you start a new character for it, but if you use a character that you used in the original campaign you lose all the gear it had for most of the first chapter. One favourite part of the "Hordes of the Underdark" expansion of Neverwinter Nights is the zero-magic area of the Beholder Caverns: all of the magical equipment and potions and scrolls and everything else you never realised your epic-level character relied on are reduced to its nonmagical equivalent. This includes the enhancement bonuses and healing items. And what do they throw at you? Level 3 to 5 Goddamned Bats. (Actually, non-demonic spiders, but still...) It's a refreshingly, unexpectedly NOT-scrappy level... unless you're a caster, but at that point, you're on the quadratic end of the equation anyway.
Divine Divinity has a segment when you're captured by The Dragon, stripped off your equipments, and thrown into prison. Fortunately, a cat (shapeshifted) comes to your rescue, and you'll be able to get your equipments back right after.
Mother 3 has you lose your entire inventory in an undersea whirlpool after a boss that just can't accept defeat. Your entire party washes up on shore with only 1 HP each, 0 PP, & whatever was equipped during the battle. A monster blocks the way and will annihilate your party in their current state. In their desperation, they resort to eating mushrooms growing near where they washed up with predictableresults. (You do get your stuff back on the other side of the jungle, though, after meeting a friendly octopus.)
Nethergate has the three Crones do this to you if you're playing a party of Celts. You do get your equipment back after escaping their maze, and it's not especially difficult. However, it takes But Thou Must to infuriating levels, since you can't get across a certain bridge to progress the plot until you go through this sequence.
In Anachronox, before fighting against the comic-book villain Rictus, he steals your mystech (magic-generating devices), limiting your options for the fight. Once you defeat him, Sly is extatic about becoming the new owner of the ginormous ship... and then remembering the twist ending of one of his comic books. Cue sudden revival, a beatdown, and the whole team being marched into the holding cells with all the other prisoners.
In Might & Magic VII, travelling to the game's final dungeon requires a brief trek through shark-infested waters while nothing but a wetsuit and a laser blaster. You can't cast any spells , either. You at least get to carry all of your armor with you, so that it can put back on just as quickly as it was taken off once you get there (which, in turn, renders the whole experience little more than a maddening exercise in completely removing everybody's equipment and then putting it right back on).
Happens repeatedly in A Dance with Rogues. It's mostly an excuse to have your character run around naked, though.
In Dragon Age: Origins – Awakening, the entire party has to fight clones of themselves wearing their equipment in order to escape, and the main character's gear is recovered last. With a bit of Sequence Breaking (i.e. unequipping all your gear before entering that dungeon—your inventory is not taken away, just your current gear), it can result in you getting free high-level gear, which the clones use in place of weapons that you were supposed to carry.
Avalon Code really rubs this in when you temporarily lose access to the item that allows you to pull weapons from Hammerspace. The character who teaches you unarmed combat does so after listing off all the weapons you've used over the course of the game, asking you if you know how to use any of them without magical assistance, while you just shake your head. (Fists are treated as a new weapon, which must be leveled up from 1 before you can do enough damage to be effective against bosses, so this is a fairly lengthy segment.)
At one point in the first Xenosaga game your party is captured and locked in a room without your weapons. But don't worry, you have chaos in your party and he gets to fight the guards on his own.
World 3-7 of Paper Mario: Sticker Star seperates you from Kersti, your Hammer, and all of your stickers upon falling in a pit of spiders. You must reclaim all of your Stickers, beat a miniboss without the Hammer, save Kersti, find the Hammer, save the Wiggler segment that fell down the hole, then finally reach the goal.
Mass Effect 3: the Citadel DLC at one point drops you into a firefight with only a level one pistol you just stole from a goon and no armour, allies or medi-gel, which is pretty inconvenient after you fall quite a long distance and get beaten down to only one health box out of five as a scripted event. Of course, you still have all of your powers, which can be astoundingly destructive if you're a power-based class, and the pistol is really quite powerful if you aim for the head.
Lunar: The Silver Star has the Crystal Tower dungeon, in which only the Dragonmaster may wield weapons due to a spell. Since no one in your party is a Dragonmaster, you have to rely on your fists and magic to defeat the various monsters within.
Metal Gear Solid: Portable Ops puts a good twist on it. As in the other games, Big Boss/Snake is captured, and stripped of his equipment... but this time, the Red Shirt Army he's spent the whole game recruiting has to search for him and break him out.
The original Metal Gear Solid only has you face one guard like this, who is easily dealt with, and then provides an excuse as to why your equipment is all in the next room over. You're being played. They wanted you to escape and use the passkey you have to override the arming system for the nuke they can't use. Being captured is part of the show, to convince you it's necessary. If the guard beats you you have to try again, so the gambit will eventually pan out.
They also hid a time bomb in with the rest of your equipment. If you don't notice the new addition to your inventory and get rid of it before the timer runs out, it explodes and you die.
One of the areas you travel through is filled with a bunch of (albeit deactivated) warheads that make firing guns really risky, so your Mission Control forces you to be unable to use any while you're in there. Not like it stops the guards from shooting at you if they catch you, though.
The final boss must be fought hand-to-hand (and the player isn't given any weapons for the escape sequence either), and the Big Bad of Metal Gear Solid 2 takes away all the player's guns before the final fight.
Reversed somewhat in the original Metal Gear. In order to rescue Gray Fox, you must trick the guards into capturing you. You then encounter the first boss of the game unarmed, and must complete a short pseudo-puzzle (while dodging the boss's fire) to get back your equipment. You can then shoot the boss with remote-controlled missiles. The kicker is that there's now a transponder in your gear that will summon endless Respawning Enemies until you discard it.
Metal Gear Solid 2: Sons of Liberty has its famous stretch where the character is stripped of both his equipment AND his clothing (leaving him stark naked), receiving strange calls on the codec.
You also have to lose all your equipment to encounter Gray Fox in Metal Gear 2: Solid Snake, but for a different reason, this time. Fox accomplishes this by setting you on fire, forcing you to go through your inventory and drop all your equipment in order to put the fire out.
Metal Gear Solid 3 has a point where you get captured and stripped of almost all your weapons, along with all your equipment and food, leaving you with only a fork and a gun with no ammunition with which to make your escape. It is, however, possible to trick the guard into giving you another weapon before attempting your escape.
Happens again in Metal Gear Solid: Peace Walker. As is common in the series, you have to enact a prison escape without your gear, though it's a little easier than the second and third games thanks to a short length and retaining CQC. In an interesting variation, you don't get all your items back after escaping. Instead, an Extra Op is unlocked where you must play as MSF soldier(s) to recover some of the items Snake had taken from him when he got captured.
Happens twice in Syphon Filter 2, where Lian escapes from an Air Force base in nothing but a hospital gown, and Gabe escapes from an Agency base after being stripped of his equipment. Both retrieve their gear towards the end of the level. There's also the third level where you need to search the truck for gear, or a psuedo example in the sewer level where you lose everything but Teresa gives you a .45 at the beginning.
Part 3 has Gabe rescuing hostages and disarming bombs carrying only a pistol while Mara's mooks wear body armor and carry automatics.
In the first bonus mission from Omega Strain, you only have a one-bullet clip to snipe the Mafia boss with, so you must use the Neck Snap to take out any bodyguards in the way without being spotted. A couple missions later, your chopper gets shot down in Mazyr, Belarus, leaving you with only your pistol and melee weapon, and you have to find the crash site to retrieve your gear, fighting through much more heavily-armed mooks along the way. In the second bonus mission, also a stealth mission, Lian Xing is undercover and armed only with poisoned shurikens; if a guard gets too close, they will see through her disguise. Then there's the Arms Bazaar in Yemen, another stealth mission that starts you out with just a knife and a civilian disguise, although you get a silenced sniper rifle and night-vision goggles early on. Done yet again in the second Yemen mission, where you have five minutes to stealth kill all the guards in the first room without them sounding the alarm.
In Thief: The Dark Project, Garrett has his gear taken away and his eye plucked out by the Big Bad. Garrett starts the level with no gear at all, but if you have the presence of mind to search the room you start in you'll easily find his bow and some other useful items.
In Thief: Deadly Shadows, the trope is played straight if the City Guards capture you, as they will toss Garrett into prison and you have to break out. This trope is also popular in fan-made missions. The difficulty depends on whether you've been depending on your weapons to get by, or if you've properly honed your stealth skills.
Splinter Cell: Double Agent has a couple. The first is fully justified since it involves escaping a maximum-security prison, and the later is hand waved with Sam saying "I wish you had given me more warning; I don't have my gear ready."
The last mission in Splinter Cell Chaos Theory has a short sequence involving the protagonist's capture; the area you're sneaking into is patrolled by guards using non-lethal weapons that KO you instead. Not as egregious as the others, as you are not actually thrown in prison, but stripped of your equipment and taken to an impromptu interrogation. When the guards enter the adjacent room, the player is given the chance to pick the lock on the handcuffs, allowing you to deal with your captors and retrieve your gear. Also, there is no Cutscene Incompetence involved; if you're captured, it's because you made a mistake all by yourself.
Tenchu: Wrath of Heaven averts this, to the point where it seems stupid. At one point in the game, Ayame winds up captured. There is nothing you can do to prevent this, as it (and her eventual escape) is part of the plot. However, between the mission where you are captured, and the mission where you escape, you are allowed to choose your inventory. Even though inventory selection is done at her base of operations. Even assuming that the inventory screen is really just window dressing and not the home base, one wonders how it is that Ayame is able to select any weapon in her entire inventory while she's locked up in prison. Stealing back weapons she had on her when she was captured, OK. Equipping weapons that she left at home before she got captured, though, doesn't make sense.
In Assassins Creed II, after Ezio's father and brothers are executed a Brute disarms him and he has to run for it. It isn't until a while later that you get the Hidden Blade, and even later before you get a proper sword again.
You start the last two levels of Hitman 2: Silent Assassin equipped with nothing but your trusty non-metallic strangulation wire.
Many levels in the Hitman series can optionally become this if you choose an approach that requires passing through security checkpoints or the like. This is especially true in later installments where you can Make It Look Like an Accident without any weapons at all.
In Dead Rising, you get captured by cultists, stripped to your underwear and put in a box. You have to break out the box and fight your way through hordes of cultists, armed with only a step-ladder (until you find the katana on a shelf). Notably, you can avoid this by defeating them at distance and thus avoiding their gas attack. This is rather difficult in most cases, although the Infinity Plus OneMega Buster renders it laughably easy. And when the Army shows up near the end, they will capture you if you "die." They strip you to your boxers and tie you up. Oddly though, even though they are there to cover up the incident, they take your pants but not your camera.
In Condemned, the final level strips the air taser that the player has had the entire game. The extremely efficient air taser that it was easy to rely on as the primary weapon through the entire game.
In Silent Hill: Homecoming, Alex begins the final level with all his (by now, considerable) stock of weapons missing. Thankfully, a quick look around the area turns up the combat knife and a basic pistol. Find an optional semi-hidden key and you'll gain access to the locker room, where all your items are conveniently stashed.
Every time you nearly fall to your death and have to climb up to safety in Silent Hill: Downpour, you'll reach the top with none of your weapons, items, or even first aid kits. You don't get your lost gear back, either; this is the game's sneaky way of keeping you from hoarding your items.
The first third of the Call of Cthulhu: Dark Corners of the Earth is played like this, and after that you still lose all your weapons in several occasions to retain the horror feel. Once you're strangely quickly given a pistol, even though the only monster in the level is utterly immune to bullets, and in other time you're reduced to a pistol, even though you would think that being sent to help a party of soldiers would call for more arsenal.
Alan Wake has the annoying habit of dropping all of his weapons, lights and ammo in between the chapters. Sometimes even in the same chapter due to cutscene stupidity.
Fatal Frame 2: Mio dropped her ghost-capturing camera after she was surprised by a ghost in the tunnel between haunted houses full of ghosts. Yeah, that's just as lame as it sounds, especially because the camera is her only "weapon" in the game. Worse, the very next puzzle can lock you with a ghost that is supposedly trivial to defeat, if only Mio has her camera.]]
In Dead Space 2, the first level consists of running past necromorphs in a straitjacket. Oh, and to make matters worse, Isaac's health bar is alarmingly low. Have fun.
Speaking of Sherry, her 12 year old incarnation in Resident Evil 2 amounts to a no gear run when you take control of her. It is justified since Sherry doesn't use weapons and thankfully, the sections with Sherry are short, have enemies that you can dodge, and she has almost double the amount of defense compared to Claire.
At one point in the Lost in Nightmares DLC for Resident Evil 5, Jill and Chris fall down a shaft and lose all of their equipment. After the fall, you're forced to wander through a labyrinth that has several enemies with the large axe. You have to use the traps that are dotted around the area to kill them.
Also happens several times to James Bond in Everything or Nothing. Quite frankly, you end up wondering why they even bother to take his weapons at all, when there are so many unlocked armouries for Bond to take his pick from. In general, Bond is infamous for this, because the enemies never take away his gadgets.
Destroy All Humans!, when Crypto's craft gets shot down in Union Town and he gets caught by Majestic.
In Oni, pretty much the whole game is like this. In the levels where you start with a weapon at all, you start with the pistol. Otherwise, you start each level with no weapon, ammunition, or hypos...even when the level transition is (as in one particular case) walking through a door, into another room. Good thing the hand-to-hand combat is so reliable...
In the original game, after getting the crap beaten out of him by Frankie "the Bat" Niagara, Max has to sneak past Frankie's men until he can get his weapons back. In order to illustrate the Bad Ass nature of Max Payne, it's important to reiterate the point: after getting pummeled with a baseball bat to the point of death, Max Payne had to escape being tied to a chair, grab the bat that had been used to whack the bejeezus out of him, use it to whack the mooks and get their guns, then go to town. It is also possible to get the mooks to shoot at each other, and finish off the remaining ones, like anyone would do in a weaponless level. Also, if you wait and observe their pattern, it is possible to get out of the basement without alerting any guards and also raiding a supply room for almost all the weapons you had lost.
In Max Payne 2, he has to evade assassins at the hospital until he can obtain a weapon from a fallen security guard and turn the tables. He also loses everything at the start of the second chapter... then the police station gets attacked.
The N64 - game Duke Nukem: Zero Hour. In the first level of the wild west episode Duke gets wrongly accused of a bank robbery and held at gunpoint by two female marshals. Of course, there's this whole alien invasion going on, but the law's the law. Duke quips how it would be a shame to shoot "the women folk", and being a well-known gentleman lets them arrest him. You start the next level in a jail cell with all your equipment gone.
At the end of the Life Missions in Heroes of Might and Magic IV, you get to keep your items but are stripped of your entire army, to fight the final end boss with just the story's main character. The enemy however, is also a lone general, who's probably lower level and has no ranks in Combat, so you can generally trounce him.
At the end of the third chapter of Fire Emblem: Thracia 776, Leaf and Lifis are thrown into jail along with Karin and Fergus ; all of them have had their equipment stripped away from them and put into chests scattered around the prison. You have to use your three new recruits with weapons (Brighton, Machyua and Lara) to get them out of their cells and to help them recover their equipment quickly, since the game mechanics allow any disarmed unit to be captured instantly.
Downplayed Trope in the XCOM: Enemy Unknown expansion Enemy Within. A group of human terrorists called EXALT are out to hinder XCOM's operation as much as they can. Neutralizing them involves locating some of their cells, and sending a covert operative to investigate them. Covert operatives cannot bring armor and main weapons on their missions, only items and a handgun. Six days later, they get the information, but their cover is blown, forcing you to send a squad to rescue your operative, or he/she will get KIA and the intelligence will be lost. While your squad can pack as much heat as you can afford, your covert operative will have to survive with limited gear and being separated from your squad.
Wide Open Sandbox
Subverted (fortunately) in Fallout 3, where despite losing all your inventory (including your pip-boy) when captured after getting a key plot item, you recover all your items from a locker conveniently placed in the room you are held in. you're even instructed by one of your captors (President Eden) to get your stuff from it. The sequence following this event, had it NOT be subverted, would've been a subversion of another fake difficulty trope (before briefly subverting/correcting itself.) Played arrow-straight, however, in "The Pitt" expansion. In order to get into Pittsburgh, you must (willingly or unwillingly) give up all your equipment except, optionally, for a hidden switchblade or the least powerful gun in the game — both are only marginally better than your bare hands despite the fact that by this point, you may be kitted out in full Power Armor with a Gatling Laser and the guards are about as strong as the other RandomMooks you've been killing for days.
Same deal for the "Mothership Zeta" expansion. Although you find some really swanky stun sticks almost immediately, and then start finding alien zap guns. It's almost enough to make you not want to bother retrieving the rest of your stuff.
Also played straight in the Operation Anchorage simulation, which starts you off with only a Silenced 10mm Pistol against virtual Chinese soldiers with assault and sniper rifles, and this time, you can't loot enemy weapons either.
The infamous Temple of Trials from Fallout 2. While you get a spear for most of it, at the end you have to go toe to toe with another member of your tribe while unarmed. If you specced for guns or other skills, you'll have a tough time. Granted, since this is Fallout, there's a few ways around it.
In the main game there are several areas with doormen that will confiscate your weapons before letting you inside (Such as casinos on The Strip or Caesar's Fort.) and hold onto them until you leave. That said, you can smuggle in small holdout weapons (like straight razors, brass knuckles, or small pistols) or large holdout weapons if your sneaking skill is especially good (like large pistols or energy weapons.) Or you can tell the doormen something along the lines of:
The Courier: "Five Words. From. My. Cold. Dead. Hands."
Note that saying that is a bad idea if you want to interact with the folks there in a way not involving gunfire.
In the Dead Money expansion, you lose all your gear from the start with the Hand Wave that the Sierra Madre automated security system removes everything with traces of radiation on it and teleports it back to your home. (Oddly enough, this does not include your Pip Boy.)
In the Honest Hearts expansion there's a more reasonable explaination - since you're joining a caravan that will travel through mountainous terrain, you can only carry 75 pounds of gear with you to keep up. (You do get to choose which gear to take with you, however. Also, if you pass a few checks, you can get someone else to carry an additional 25 pounds of gear for you.)
During the first leg of the quest "Still in the Dark" (unless you have Veronica as a follower), the Brotherhood of Steel strips you of your inventory as well as fitting you with an explosive collar, and sends you to deal with an NCR ranger using just your speech, repair, or unarmed combat skills.
In order to complete the "Penal Ties" mission in the Residential district of Grand Theft Auto 2, you have to get arrested, and thereby get stripped of all your weapons.
The last story mission of Grand Theft Auto III sees you stripped of the possible thousands-of-pounds of weaponry and ammunition you might be carrying in the opening cutscene before you punch out a guard and steal his pistol. The rest of the mission requires you to keep pace with your fleeing ex-girlfriend turned crime lord while properly re-arming yourself to stay alive and eventually shoot down the helicopter she's escaping in. If the player finds many of the packages and is swift with a vehicle, it is possible to swing by a safehouse and load up on the goodies.
In general, the installments from Vice City on, on account of having a Limited Loadout you can swap out for different guns, will often take your stronger weapons and replace them with weaker ones as a story necessity, thereby cheating you out of your hard-earned equipment.
In Grand Theft Auto: Vice City, Tommy is asked to persuade someone to part with some land by going to the country club and beating the crap out of him. There's a metal detector at the entrance which places all your weapons outside (you can pick them up again when you leave) — but this trope is subverted because it is possible to jump over the outside wall and enter the country club with all your equipment. The metal detector only takes away your guns and grenades, though. Entering with a chainsaw is perfectly fine. This happens in the airport terminal, too, and you can't get around that one.
In Grand Theft Auto: San Andreas, CJ loses all his guns several times. After you've finished the story missions for the first city, you're dumped out of town with no weapons. Later on, after the helicopter he's gunning down from gets... gunned down and crashes in water. You must then make your way aboard the gangster-ridden container ship you were attacking and acquire guns by killing gang members. (Or you can simply swim ashore, buy new weapons, and go back). Another mission, Stowaway, has CJ inside a plane loaded with explosives (possibly landmines). Shooting in there is not forbidden, no - but one shot that misses a government agent mook in there means hitting the explosives and the whole thing goes kaboom. Players are likely to resort to melee weapons or unarmed combat in there, risking no such thing - especially since getting into the plane in the first place is That One Level Part players are unlikely to want to repeat. note Driving up to and then up a narrow ramp of said plane, while it's taking off, on a motorbike, and with barrels rolling out of the ramp every once in a while. And the plane has quite a lot of head start...
Scarface: The World is Yours does this in the mission where Tony returns to Freedomtown, confiscating his weapons and springing an ambush on him. It also does... something like this at the start of the assault on the Very Definitely Final Dungeon, dropping all the stuff in Tony's Hyperspace Arsenal for a Desert Eagle and rather limited ammo. You have to collect guns off fallen enemies to keep fighting.
Minecraft has you drop all of your items upon death, which means you're forced to endure the game without any weapons or tools when you respawn unless you are quick enough to get back to where you died or had stored extra items away in a chest. Many custom maps that take advantage of Command Blocks can also strip you of all your items if the block is programmed to do so.
Can be subverted, though, as the game does include a command line prompt that prevents this. Again, use of Command Blocks can also enable this ability.
In the story mode of Yu-Gi-Oh! 5D's Stardust Accelerator, the player gets sent to jail after breaking into Neo Domino City, duel runner and cards confiscated in the process. While you use borrowed cards to win your freedom, it takes a little Stealth-Based Mission to get your stuff back.
While your weapons are bolted onto the ship and cannot be removed, Warship Gunner 2 has one mission where your ship has expended all of its ammunition and needs to resupply by taking over an enemy depot (presumably with a contingent of marines). Fortunately, the only opposition comes from coastal defense guns that are more annoying than anything else.
In the final four races of the 6th-gen Test Drive reboot, the game takes away all your previous cars and has you race an ancient Ford GT-40 against a Dodge Viper Competition Coupe.
In several levels of the Driver series, e.g., "The President's Run" and "Chase the Gunman", you are given a slow, clunky car and forced to flee from or chase much faster opponents.
Happens bizarrely enough in Tony Hawk's Underground, where you surrender your skateboard to go and get your friend's skateboard back from a bunch of drug dealers. Essentially this is an excuse to give you a tutorial on the off foot mechanic.
In LEGO Lord of the Rings, in keeping with the movie, you can't go before Theoden King so armed, by order of Grima Wormtongue. Aragorn, Legolas and Gimli have to fight guards with their bare hands or with conveniently placed candlesticks. Thankfully, Gandalf has his staff and if you heal Theoden quickly you won't be without your gear for very long.