For the sake of clarity, this post will not deal with swords that are also guns, other than to say that they are awesome.
In the real world, there are swords and there are guns, and there's really no point in comparing the two. While there are apparently still some people out there who kill other people with swords, these people are usually insane enough for it not to count. Plus, modern-day sword-using killers tend to kill people who are unarmed and not particularly interested in fighting back. If someone with a sword tries to fight someone with a gun, the results are unlikely to surprise anybody.
When you take the realm of fiction, however, the situation is often reversed. This is partially because fictional worlds operate not so much on stodgy systems of "logic" than on systems of "awesome," and partially because the protagonists of these stories need a challenge that usually isn't offered by gunning down sword-wielding enemies from across the room.
Giving your protagonist a sword when his enemies all have guns is a good way of establishing his badassitude. Whether he has to rely on his sneakiness, his forethought, or simply his bullet-dodging acrobatics, he's going to be the underdog, which makes his victory that much more impressive. As an added bonus, the anachronism of using such an elegant weapon hearkens back to a more civilized age, so our hero gets the associated ideals of honor, duty, etc.
So far, so good. If you're writing a book, comic book, or movie about a guy who uses swords to fight guys with guns, it's not going to take a whole lot of explanation for me to say, "Okay, you've got me sold, now let's see some violence, plz kthx." This is an advantage to the "my story, let me show you it" method of storytelling: total control over the plot lets you sacrifice logic for the sake of awesome thanks to the underlying assumption that, if this was anyone else with a sword, they'd be shot to pieces in five seconds, and it's only because our hero is so skilled, trained, lucky, and badass that he gets to carve up his enemies instead.
Of course, there is another method of storytelling that we nerds experience, and that is the "my story, plz tell it to me" method found in video games and roleplaying games. In this method, the system is laid out for you, but it's up to the viewer to generate the actual events. This means that, rather than being able to say "99% of the time gun beats sword, now let me show you the 1%," you have to set up a scenario in which sword always beats gun, or at least stands a good chance against it. And this is where things get weird.
Perhaps the most famous example of this is Final Fantasy VII, in which a guy with a sword (Cloud) does a crapload more damage than a guy with a gun (Vincent). Then you've got systems (see: D&D) where a great big sword is going to be doing more damage than a gun. One wonders, therefore, why anyone would bother using, or even inventing, a firearm, when a sharpened piece of metal is more effective.
There is a reason behind this decision, however, and it deals with the main underlying difference in combat in video games and RPGs versus real life (or media based on real life, such as novels and movies). In real life, it takes a single good hit to take someone out of a fight. This hit could come from a sword, a gun, a rock, or a Scud missile: the result is the same. Death. In video games and RPGs (and RPG video games, and RPGs based on video games), a single good hit is going to hurt your opponent, but they will keep fighting. They lose hit points, but they are not dead, and now it's their turn to hit you.
So while real life combat operates on a more or less binary system of damage (dead/not dead), video games and RPGs have to come up with a sliding scale of damage ('tis but a scratch through MASSIVE DAMAGE). Realism goes out the window, and now we have to decide whether a bullet to the chest should do more or less damage than a sword to the chest. Looking around for something to base this decision on, we come across the previously-mentioned principle of "awesome," and naturally decide that a sword should do more damage.
Because, fundamentally, it's cooler to stab someone than to shoot them.
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