It's not easy being The Hero. Sir Bob has to worry about Saving the World from Baron von Evilpants, and his Legions of Hell. So, after a climactic battle, Sir Bob decides he deserves a good night's rest at the local Trauma Inn. Too bad it isn't guaranteed (especially if the innkeeper tells you it's on the house). Sir Bob will either...
The most obvious sign of Inn Security segment is when party members make a big deal about resting somewhere, or the inn NPCs make a big deal about having party members rest in the Inn.
It usually takes place during the beginning or middle of the game, supposedly to provide a little more backstory for the sleeping character.
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In the second book of Sorcery! (a series of four linked Fighting Fantasy gamebooks) you normally end up staying at an inn, and wake up tied up to an elaborate trap created by the innkeeper. Make the wrong choice and a guillotine blade decapitates you.
In The Lord of the Rings, the events at the Prancing Pony make Strider paranoid enough to have the hobbits sleep in his room instead of their own. This turns out to be a good thing; in the morning they discover the hobbits' rooms have been ransacked and the stables opened and their ponies gone; both the Peter Jackson movie and the much-maligned Ralph Bakshi movie depict the Nazgűl sneaking into the inn and attacking the hobbits' room.
In the first Wheel of Time book, Rand and Mat are trapped in their room and nearly killed by a darkfriend and his goons in the village of Four Kings. They're saved at the last second by a freak lightning strike caused by Rand unknowingly channeling the One Power.
In the fifth Slayers light novel, Lina is enjoying a peaceful stay at an inn when Mazenda tries to kill her by burning the whole building down. She escapes by jumping out a window.
In Stardust, Yvaine is taken in by the kindly wife of an inkeeper and looked after. Unfortunately, the "inkeeper's wife" is really a witch queen who wants Yvaine's heart to make herself young again and the whole inn is an elaborate ruse to that end.
The protagonist in H.P. Lovecraft's short story "The Shadow Over Innsmouth" is attacked while staying at an inn in the eponymous town. He is sufficiently restless/paranoid that he barricades the room long before they try to enter by force and escapes without even getting a good look at his attackers until later on.
In The Redwall Series, while Inns don't seem to exist in that universe, there have been countless situations where characters bunking down (Whether in the wild, or staying at someone's home) wake up captured. Though it works both ways, many times Mooks of the villains wake up being captured by the heroes.
Murderess features Chopped Tree Inn, where Lu stops to eat and rest. She’s greeted by a boy speaking in Creepy Monotone, a mysterious figure which may or may not be malevolent gives her some basic details about the Land of the Sea, and she’s awoken in the middle of the night to be given some instructions on her journey in a rather creepy way. Subverted, as she was never in danger the whole time; the mysterious figure was Déaspor, who is one of the good guys.
Alluded to in The Sleeping Beauty: the innkeeper of the inn Leopold takes Siegfried to pays a magician to keep an anti-thief spell on the inn at all times. It's not cheap, but he makes it back with the guarantee that his customers won't get robbed in the night.
There's a Dungeons & Dragons Monster Manual (Creature Collection, if anyone's interested) that has a monster that practically embodies this trope: the Inn-Wight. It's a ghost that haunts an inn, and sneaks into beds. Whoever has the misfortune to sleep in the same bed as an Inn-Wight is drained of life. Just proving that in D&D, everything is trying to kill you.
An example of the first comes from Final Fantasy IV: An hour into the game, Dark Knight Cecil carries an unconscious Rydia into Kaipo's Trauma Inn. While they're sleeping, the Baron Guards burst in and attempt to kill her. Much asskicking ensues.
Later on, the second type occurs when Edward faces down the Fake Anna. It would be a Duel Boss scenario if a) the doppelganger were not just an ordinary mook, and/or b) Edward wasn't (at that point in time) a total wuss in combat.
And in Final Fantasy IV: The After Years, the same thing happens in a major case of Deja Vu, with Baron soldiers attacking Ceodore and the Hooded Man in the same Inn.
Surprisingly averted in Final Fantasy V, when the party travels to the character Bartz's home town and are offered a free stay at the inn, no plot or strings attached.
Free Inn Rule. When an inn is free for no reason, don't stay there. Somebody will steal your money during the night. Does not apply to inns that are free for a reason (i.e., you saved the town, main character's hometown, etc.).
When you rest for free on your first visit to Figaro, the party awakes to find the castle under attack by Imperial troops.
The inn in Vector is free; however, there is a chance for the innkeeper to steal several thousand Gil from you while you sleep.
The proper place to heal is a smaller unmarked building. The owner there, on the other hand, tries to kill you. But fortunately, after taking out their mooks, are more cooperative. In a way both playing the trope straight and subverting it.
After Strago provides you with a cheap stay at the inn (one gil) in Thamasa, the party is forced awake in the middle of the night to rescue Relm from a burning building.
This one is a subversion, since the one-gil price is maintained for all future visits to Thamasa.
If the party rests in the ruins of Doma after the Cataclysm, and Cyan is in the party, he becomes possessed by a monster and the rest of the party must enter his dreams to free him.
Subversion: If you have Shadow in your party, and find any ridiculously underpriced inn, DO stay there: You will be treated to a scene on Shadow's backstory.
Final Fantasy VII had a stay in an old woman's house. Unusual as it isn't until morning that Cloud wakes up, and when he does the event has no real sense of urgency.
Earlier in the game, he is allowed to sleep at Aerith's house. He has a text-only Dream Sequence, heavy with Foreshadowing, and then wakes up in the early hours of the morning and has to sneak out under Aerith's mother's orders.
Final Fantasy XII has both the "bad/plot stuff when you try to heal" and the "free use of normally pay-per-use mechanics equals plot relevant" sides of the trope, independently of each other.
The "heal" side pops up in the form of "Crystal Bugs", who looks just like the save-heal-and-teleport crystals you usually use — untill you try to use 'em, and instead find yourself under fire. Particularly sneaky since you're liable to be short on HP at that point...
The "Free" side happens when you first leave Jahara. You are offered a free chocobo rental, and about five cutscenes later (well within the rental time if you don't dawdle), you're required to cross a chocobo only path to go farther in the plot.
In the Gameboy game Final Fantasy Adventure (also called Seiken Densetsu: Final Fantasy Gaiden) you can sleep for free in a certain castle, but when you do the girl that you've had tagging along with you will be kidnapped by a vampire.
Naturally, the same thing happens in the much later remake, Sword of Mana.
An innkeeper tries to rob you Breath of Fire, but if the characters has a certain item in their inventory — a purse that's described as impossible to steal — they will catch the innkeeper robbing them and effectively blackmail him for a large amount of gold.
There are a couple of examples in Super Mario RPG: Legend of the Seven Stars:
A free stay in Rose Town ends up with the innkeeper's son's toy coming to life and wandering out into the woods, prompting Mario and company to follow. (Said stay is free because, while it was still a toy, the innkeeper son accidentally uses it to KNOCK MARIO OUT.)
Before you save the townsfolk at Seaside Town, staying at the inn is free...if you can handle the phony innkeeper's creepy voyeurism as part of the deal.
After you save them, though, the innkeeper will let you stay, even if you don't have enough coins to pay the fee.
The Three Musty Fears would like to play a flag game with you, but only if you stay in the free Monstro Town Inn.
Star Ocean: Till the End of Time has the team waking up from a free night in an inn to realise one of the party members has snuck out to go on a suicide mission.
And if you're so inclined to get one of the optional party members, you get woken up in the middle of the night by said optional party member stabbing your pillow an inch from your face.
Star Ocean: The Second Story has an aversion. You get to stay at an inn for free early in the game and...nothing really happens during the night. Rena wakes up to spy on Claude, but that's it.
Tales of Phantasia used the trope both directly and in variation repeatedly. Near the beginning of the game, you have to rest at your uncle's house, and the resulting cutscene kicks you into the dungeon. On the other hand, the game also offers you a free rest when something has to happen "tomorrow" or "in a while," such as when you're waiting for an NPC to return to the inn to meet him, or when your characters decide to meet in the inn to discuss the plan to infiltrate a castle (well, the first one's free - you have to pay to visit the cutscene if you decide to hold off on the mission).
This is generally subverted in the "Tales of" series. You are frequently offered free rests at inns, but the result is almost never dangerous or detrimental. More frequently, it is used to advance the plot.
In Terranigma you are required to go to bed four different times. The first two and the fourth are free, but the third isn't: after the game instructs you, you'll have to pay the usual pittance to go to bed.
In one of these, it seems kindly enough, but the town turns out to have a dark secret: namely, that everyone in it is the living dead, and the town's living appearance is a mirage generated by one very powerful little girl.
In Sword of Vermilion, the inns cost a surprisingly high amount and only get more expensive as you go. This makes the free inn in a cursed town seem awfully tempting... but for each time you abuse the hospitality of the absent-minded owner, he'll jack up the price of the inn when you finally break the curse.
Speaking of Oblivion, if you choose to stay in an inn in (say that out loud three times fast) the Imperial City, it's not only attacked but, because it's actually a boat that's just been tethered to the waterfront, it's also put out to sea thereby forcing you to kill the raiding party just to get back to land. You do get a cool-looking sword out of it, though.
The tradition continues in Skyrim. If you do what Aventus Arentino in Windhelm says, which is to kill Grelod the Kind, a courier will eventually come and deliver an ominous note. If you fall asleep for any length anywhere, be it your home, at an inn, or in an anonymous bedroll, Astrid, the leader of the Dark Brotherhood, will kidnap you and bring you to an abandoned shack to begin the Dark Brotherhood questline.
There are three quests in Oblivion that will wake you up almost immediately to tell you whatever: the Hermaeus Mora Daedric quest, and the starting quests for the Thieves' Guild and the Dark Brotherhood.
Should you happen to get a room at Moslin's Inn in Hackdirt while looking for Dar-Ma, you will be rudely awoken by a bug-eyed creep trying to club you on the head.
The Benrius Manor house quest has the player chased out of his slumber by the resident ghosts. Undead are bad enough, but when they won't let you sleep? The worst.
In Elder Scrolls 1 Arena (Or was it Daggerfall?) There is a glitch which if you sleep in an inn, there is a rare chance you'll be locked in your room and you can hear guards telling you to surrender on the other side.
In MOTHER, sleeping in the hotel in Spookanne/Halloween is free... but you have to fight a Starman in the morning, and, since the Starman was disguised as the innkeeper, you can never spend the night there again.
There is also a variation in EarthBound, where zombies take over the local Trauma Inn to trap you there. But they don't wait for you to go to sleep.
In Neverwinter Nights 2, you get attacked at an inn once. However, it is relatively unimportant to the plot and the inn is one of your bases of operation.
The Hordes of the Underdark module for Neverwinter Nights starts out with you waking up while a Drow steals all your equipment, teleporting it away before you kill her. You even have the option to spend the rest of the game bitching about it and claim its your only motivation in taking on the Matriarch. Eventually you can find them all in a chest in the level before you meet the crazy mage.
In Dragon Quest VIII, there are some places where you can sleep for free, but most charge. A free night at one of the places which normally charges ends with one of the party members having run off having been possessed by the Sealed Evil in a Can.
In Romancing SaGa, this can occur in South Estamir after/if you've agreed to investigate a reviving assassin's guild. This can turn into a Player Punch if you're currently playing as Jamil... if you let Dowd leave beforehand.
In Skies of Arcadia, the only times you'll ever get the chance to sleep for free (outside of your own base or your mom's house) are when something plot-relevant (and usually dangerous) happens as soon as you wake up.
Not quite an inn, but in Seiken Densetsu 3, there are ferries between towns early in the game costing around two hundred lucre per trip. It's free twice: once to flee an occupied city during the prologue, and once where you will wake up in the middle to find yourself on a Ghost Ship. Truer to the spirit (ahem) of the trope, once on the boat if you choose to sleep in any of the provided beds, you will be attacked by monsters before you get any rest
In Suikoden I, on Mt. Tigerwolf there's an Inn the player stops in. It soon becomes obvious that the Innkeep is up to not good when you are But Thou Must into drinking the tea (which naturally knocks everyone out). Of course, everyone's okay because the guy's boss recognizes one of you and forces the Innkeep to make an antidote.
Later on, your party will avert another guy's attempt to Drug-and-Rob you in an Inn.
While healing up at a Pokémon Center is always free, if you get the special item for the Darkrai event in Pokémon Diamond and Pearl, you gain entry to a hotel where you're immediately beckoned to sleep...then proceed to wake up on Newmoon Island where Darkrai is waiting.
Somewhat averted in Ruby/Sapphire/Emerald on one of the routes an old lady suggests you spend the night, well, okay. As soon as you wake up she suggests you spend the night again, this repeats infinitely until you say no. As suspicious as it seems, that's all it is suspicious. She doesn't rob you she just enjoys you spending the night. Which thinking about it too hard could fall into Fridge Horror.
Not an inn, but your party camp effectively serves as one in Dragon Age: Origins. About 2/3 of the way through the game, Shrieks will attack you in the camp, one of the few times every party member can participate in a combat at the same time. There's additional plot revelation if you're a Dalish elf.
Most inns in Betrayal In Antara charge you, but there are two exceptions. First, the inn owned by Aren's parents, which is very useful in all chapters you can get to it, and second the inn you stay in in chapter 3, but only after you have triggered all the major plot flags for the chapter. That time, you don't get charged, but you do get woken up in the middle of the night and dragged into the next chapter.
In Paper Mario: The Thousand-Year Door, you can ride the Excess Express for free, which leads everyone in the party to figure that all you'll have to do to get the last Crystal Star is take a luxury train for a three-day ride. Over the course of those three days, you have to help a ghost move on, find some stolen items, foil a bomb plot, find Doopliss and bust his disguise, unblock the train tracks, and finally save the passengers from some creepy, black monster things. Of course.
Subverted in Golden Sun: Dark Dawn, which openly plays up the "oh shit something's going to happen" factor when the party discovers that the city of Harapa is barricaded at night and they're stuck until morning. Sleep at the inn... and in the morning everything's back to normal. Subverted again during the Grave Eclipse, since the barricades are automatic and triggered by darkness, so now all the survivors are sealed into the town... but at least the monsters outside the town can't get to them there.
Averted in the adventure game Darkstone, in which you can spend a night (for about ten seconds) with Perry the Publican to completely restore your health and food levels.
Magicka parodies many RPG tropes and exaggerates this one. Staying in the inn in Havindr is mandatory and you'll be woken up by a meteor smashing the inn!
In Return To Krondor, towards the middle of the game you have a wide open world map (actually a very tiny corner of Midkemia, especially compared to Betrayal at Krondor) to explore for a while to get some grinding and looting done before getting back to the main plot. You have to stop at an inn near the center of the world map for a much-needed rest and restock... only for the place to be set on fire and turn into a combat encounter before the night is over.
Ordinarily this is averted in Neverwinter Nights 2: the Sunken Flagon, your base of operations in Neverwinter, is pretty safe due to being frequented by adventurers and off-duty Watch officers. The exception comes at the end of Act I, when the githyanki that had been bothering you periodically for the length of the chapter attack the inn and kidnap Shandra Jerro because they think she has information about some plot coupons.
Dragon's Dogma gives you a free night at the inn the first time you rest at The Encampment in the beginning of the game. You're then woken up by a hydra, of course.
Happens near the beginning of No Need for Bushido when Yori and Ina stop at an inn. The "Foreboding Ninja Death Inn," to be exact. Lampshaded later:
Ina: I say we find a place for the night.
Cho: Perhaps one without ninja assassins?
Ina: There was once a time when I thought that was possible.