When you think of science fiction and video games, there are a few obvious titles which jump out, Halo, Mass Effect, Half-Life, or Fallout being just a few examples. There is, however, an extremely famous series of JRPGs, which I would argue have a ton of science fiction influences, most of which have somehow flown under the radar of the general public. That series (as you've probably realized if you read the article title) is Pokémon.
Pokémon, in case you've been living under a rock, is a series of Japanese monster collecting JRPGs which exploded in popularity world wide when they hit the scene in the late 90's. The craze eventually died down (for a time it seemed you couldn't throw a Geodude without hitting a piece of Pokémon merchandise), but the franchise has still retained immense popularity, now including (but not limited to) an anime series which recently passed over 800 episodes, a whopping 16 movies (with a 17th hitting Japanese theaters this summer), dozens of manga, and a roster of creatures now set at over 700. That's not even to mention the dozens of games, including spin-offs.
The game series involves capturing Pokémon, and training them to battle others, collecting various gym badges through what amount to boss battles, and completing a "pokédex," by collecting all of the creatures. The series is known for being adorable and kid friendly, just a little bit messed up, and surprisingly deep at a competitive level.
What it's not really known for is being a science fiction franchise, despite many examples of advanced technology, and even close encounters.
Let's start with the most immediately obvious example, the pokéball.
The iconic pokéball is the device which is used to capture Pokémon. It's just large enough to fit in your hand, and yet it is capable of holding creatures roughly the size of... something really, really big.
How, you ask? Well, it appears that the Pokémon are being converted into energy, stored within the ball, and then restored back into a living form of matter. In the anime, when a Pokémon is returning to its ball, it briefly turns into red energy, before entering the ball.
Similarly, when a Pokémon enters or leaves it pokéball in the game, a flash of white light appears, presumably showing the same effect. It's clear that these massive creatures are somehow being kept in some sort of stasis when they enter the pokéballs.
For that matter, the games and anime also have a vitally important feature called the PC, found in every Pokémon Center, which not only allows you to store a much larger number of Pokémon, but allows you to access the Pokémon stored at one location from any other location. In other words, it's breaking solid matter down into energy, transporting that energy across the world, and then reconstructing it elsewhere. We're talking about functional teleportation, here.
If calling that a teleporter seems like a stretch, let me point out the context in which you first meet Bill. The creator of the Pokémon Storage System (otherwise known as the PC), Bill, was a character you could meet in the very first Pokémon games. In a scene straight out of The Fly, Bill had been transformed into a Pokémon while experimenting with an invention called a transporter. This malfunction might explain why the PC system is used only on Pokémon, and not for human travel (the absolute best way to travel in the Pokémon universe is by flying on a Pokémon's back, of course).
Even if you don't like the PC System example, there's plenty of other examples of advanced technology in the Pokémon universe. Technical Machines and Hidden Machines (TMs and HMs) are devices which allow you to instantly teach your Pokémon specific moves, meaning a machine which can instantly give a creature knowledge is a thing which exists in the Pokémon universe. The healing machines which Nurse Joy uses to heal a players Pokémon in the game are capable of instantly healing wounds, as are special items like the Potion (and Super Potion, and Hyper Potion).
While Pokémon Colosseum wasn't developed by Gamefreak and might fall into debatable canon territory, the first game even featured the main character frequently riding an awesome hoverbike.
If we really want to stretch into the "debatable canon" realm, the second generation of Pokémon games, Pokémon Gold, Silver, and Crystal, contained a special device available in Pokémon centers called a "Time Capsule," which was able to pull Pokémon from the original games into the newer ones... Although, whether this should be taken as anything more than a game mechanic is debatable. Bill does show up again calling it his latest invention (a time machine), but this was struck from the remakes of G/S/C, replaced by the Pokémon Wi-Fi Connection.
In addition, while I'm focusing primarily on the games (since that is what I'm most familiar with), the anime has other examples, including a ton of giant robots. The fourth movie, focusing on Celebi (a time-travelling forest protector) featured a (spoilers!) young Professor Oak being brought to the present, and using what amounts to a steampunk pokéball.
Whether this was the former standard form of pokéballs, or just a cobbled together version created by the young Pokémon professor is never made clear.
Even some of the Pokémon themselves are great examples of advanced technology. Porygon is the most obvious example, categorized as the "virtual Pokémon."
Porygon is an entirely man-made Pokémon. The Ruby pokédex said that Porygon was "capable of converting itself entirely back to program data and entering cyberspace," while the more recent X pokédex said that Porygon "consists entirely of programming." In other words, scientists of the Pokémon universe were actually able to create a living program, and then turn it into a solid, physical life form (presumably using the same method that converts Pokémon to energy and then back). Furthermore, as the series went on devices called "upgrades" were able to be used on Porygon to essentially upgrade its software to the more advanced Porygon 2, and a dubious disc of data was created which would corrupt Porygon into its final stage, Porygon-Z.
The most obvious and famous example of a man-made pokémon, though, has to be the star of the first Pokémon movie, Mewtwo.
Mewtwo was created as a genetically altered clone of Mew, the first genetic ancestor of all Pokémon. In the anime it was created by Giovanni, the leader of Team Rocket (who gave it an awesome suit of psychic armor). Things didn't end well.
In the games its origins are a bit more cryptic, involving the ruined mansion on Cinnabar Island, but it's still clearly a genetically altered clone of Mew. This means not only is cloning possible in the Pokémon universe, but it's possible to genetically engineer entirely new species of creatures. This is basically the plot of the movie Splice, right? I don't know, I never saw Splice.
So there's plenty out there to prove that the Pokémon universe has far more advanced technology than our world does, but what about those close encounters I mentioned earlier? It turns out some of the Pokémon might not actually be of our world.
I'm going to break these into the same four categories which Bulbapedia does, and we'll talk about the Pokemon out there which are confirmed to be otherworldly first.
There is actually only one Pokémon which is 100% confirmed to be from outer space. That Pokémon is Deoxys, the DNA Pokémon.
Deoxys is an alien virus which fell to earth on a meteorite, and underwent a rapid mutation into a Pokémon. It's appeared in the anime, most notably in the seventh movie Destiny Deoxys, and was introduced to the games in the third generation. The pokédex entries on it all agree that it was an alien virus which fell to earth, was exposed to some kind of laser, and underwent a rapid change.
While Deoxys is the only confirmed extraterrestrial Pokémon, there's a surprisingly large number of extradimensional Pokémon. Probably the most notable of these are the Unown, Giratina, and Arceus.
The Unown were introduced in generation two, and while they're actually really underpowered Pokémon in the games, their power really shined in the third Pokémon movie, Secret of the Unown. In this movie not only were the legendary Unown unleashed on an unsuspecting Johto town, but an archaeologist who studied the Unown was transported into their own, seemingly nightmarish dimension.
Giratina, meanwhile, is a legendary Pokémon native to a dimension of antimatter, the exact opposite of ours, known as the Distortion World. It was supposedly banished there by resident Pokémon god Arceus for being too violent. It's basically Pokémon satan, so have fun with that.
The last confirmed extradimensional Pokémon I'll mention (and this might be a stretch) is Arceus, who I alluded to a moment ago as the god of the Pokémon universe. While we're delving into more fantasy territory here, if Giratina is the devil, and the distortion world is hell, Arceus' Hall of Origin is heaven... Though there's never been a legitimate way to access the zone. So getting there requires cheating.
"It is described in mythology as the Pokémon that shaped the universe with its 1,000 arms." "It is told in mythology that this Pokémon was born before the universe even existed." "According to the legends of Sinnoh, this Pokémon emerged from an egg and shaped all there is in this world." I wasn't kidding about it being the Pokémon god.
While these are the most notable Pokémon which have confirmed alien origins, there's several others which are believed to be extraterrestrial.
Probably the most famous of these is Clefairy, due to an early episode of the anime ("Clefairy and the Moon Stone") which featured a scientist named Seymour who was convinced that Clefairy had come from the moon. Clefairy has not only been shown to have high intelligence in the anime (constructing aircraft which look a lot like traditional UFOs), but to be obsessed with the moon, living in Mt. Moon, evolving via Moon Stone, even going out during full moons to dance under its light. The pre-evolved form of Clefairy, Cleffa, is also associated with space, although more with meteorites. Cleffa are said to appear more often during meteor showers. They're also often found around the craters of meteor strikes.
Another pair of Pokémon associated with space which I'll talk about are Elgyem and Beheeyem.
The first thing you'll notice is that they're literally called LGM (Little Green Man) and BEM (Bug-Eyed Monster), two common terms for aliens. These two were supposedly only recently discovered in the Pokémon universe, 50 years before the events of Pokémon Black and White. They were first discovered in the desert (near a supposed UFO crash site), but migrated to a new location at the Celestial Tower.
These two first appeared in Pokémon Black and White, which were set in the Pokémon universe version of America, and they are obviously references to the Roswell conspiracy.
I've really only touched on some of the more obvious points here, but there are plenty of other examples of Pokémon crossing the line into sci-fi. While it's certainly on the softest end of the sci-fi hardness spectrum, it still qualifies in some surprising ways. Actually, it probably contains more examples of traditional science fiction tropes than even the often compared Digimon, which was actually set in virtual reality (I'm talking about Digimon Adventure 01 and 02 here, for Digimon nerds like me. Tamers had a lot more sci-fi elements to it, and was great for it.).So just keep in mind, not only are the creators of Pokémon slipping in disturbing lore about child abductions and bizarrely tragic backstories, they're developing one of the most popular science fiction series out there.