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Every good hero has a fatal flaw. Even Superman has kryptonite, and is arguably kindof a coward.

For your speedster, maybe he's not very good at forward-thinking. The non-speedster only has to set up some bait and swing his bat -- the speedster hits the bat every time, and at those speeds, the blow does a lot of damage.

For that matter, your speedster can't afford to take a hit while he's moving fast at all. Even if a bug gets in his way, it'll be like a paintball or a bullet, depending on his speed. The non-speedster just has to throw some sand in the air, and it'll disintegrate the speedster as he moves through it.

We can add some real science back into this to help handwave some things. Science and handwaving, what fun!

This speedster is fast, real fast, but where do they get the calories to burn for this speed? The faster they go, the more calories they need. Let's make a ballpark figure and say at full near light speed, they are burning 1000 calories a second. At this rate, an opponent merely needs to wait for the speedster to starve themselves and fall asleep or die. This means the speedster can only operate in short prepared bursts and must stop frequently for food and water. They can't just run around the world, they would burn up all their muscles before they got half way over the ocean.

And there you go, a plausible limitation that lends itself nicely into multiple possible story puzzles for heroes and villains to solve.

Even assuming the Flash got all the powers he needed, super stamina, near indestructable body, etc, A real-life Flash running at hundreds of miles an hour would actually have several weaknesses just from the laws of physics.

IRL, there are a few major problems with running super fast. Many of these problems would severely limit a speedster superhero. Both Friction and Inertia would be his enemies.

Pants on Fire - In reality, I doubt any material is both flexible enough to withstand moving at hundreds of miles an hour, and frictionless enough not to burst into flames. The Flash will have to slow down if he wants to keep his clothes on.

Cool-Aid Man Stops - Remember how the Cool-Aid Man breaks through the wall to hand out cool refreshing sugar-water. Unlike in the comics, where the flash can run up buildings, inertia means he'd likely run through the wall, shattering it or himself into pieces.

Skid Marks - Running straight is easy, but every time he turned, he'd leave deep indentions in the grass, broken pavement, and the like. It would be pretty easy to follow him to his secret crime lab.

Turning on a Dime - Similar to above. The Flash would not be able to turn quickly given his inertia and small mass. Simply block stright-aways and the Flash has to go MUCH slower. Throw in some trip wires and obscured holes and you'll probably be able to nab yourself a speedster.

Follow the Fire (and Noise) - Running super fast will create friction (i.e. heat) with the air, even if the suit is frictionless (see #1). He'd also likely sound like a sports car zooming past. A heat-guided missile + some other smarts would probably have no problem locking onto him.

Calorie Deficit - Marathon runners burn about 2,500. . That's a few minutes of running for the Flash. Simply pay off pizza and burger joints to find out who the skinny guy is that eats 5 burgers a day, and you'll unmask your hero.

How do you say Adamantane - The Flash will need a special suit + special communications devices that work at his speed. Those will be one of a kind. Simply follow orders of exotic materials until you find the crime lab.

Don't use the Flash.

You are right speedsters like Flash are too OP. But it is cool to have people who are really quick. It might be even cooler to have them be just past the edge of what is humanly possible. My suggestions

1: Think of things you want your Speedster to do. For example, a person who could process fast and move fast might be just about impossible for a normal person to catch / hit. I know because I lived with a guy like that. After he ate your food he would head off across campus, giggling, staying just 10 feet in front of you, and sometimes even lying on the ground. But he could always scramble up and get away before you caught him. You would need a team to do it and by the time you assembled them he would be gone.

2: Rule out impossible QuickSilver type stuff.

3: Figure out weaknesses. For example someone who thinks and acts really fast might not take the most prudent course of action. Like failing to have a line of escape set up when he set about eating all the BooBerry cereal.

4: Defeat the speedster. Normal speed person can defeat the speedster by exploiting those weaknesses with a trap or the like, or an endurance contest. Or failing that having a team to surround him. Or coopt the Speedster to your side (BooBerry might work).

Most answers have focused on weaknesses of high speed, I'll try some things against high powered speedsters.

Your typical superman, quicksilver and flash often spend more time in normal speeds than superspeeds. Bring a high-velocity weapon like a powerful laser to the battle and fire when they are moving normal speed. If you intend to do an Evil speech first, disguise the laser in your suit or clothes so by the time the speedster sees what is about to happen he's already being burned and possibly blind. An easy target.

NBC's, Nuclear, Biological. chemical. You are fighting super-powered beings, take your time killing them! If you can get your hands on them you could set up a scenario where the speedster will cross a radiation area with enough radiation to kill in months... Or if you have more it might kill in weeks, days or even minutes even if the speedster exits the field. Unless the speedster has a geiger teller with him he (or she) wont even know he was radiated and dying.

Biological is another one. A powerful disease could sicken the target without the speedster knowing. The disease could be lethal, or cause deleriums that are harmless to normal people but to a speedster could cause problems if he uses his powers. Or just weaken him for you to finish.

Chemical is probably where it's at. A speedster's body might be able to speed up its immune response against virusses and bacteria, but if his body speeds up carbon-monoxide poisoning you are farther from home and something like that often happens unnoticed, especially in a scenario where the speedster is busy with other things and their fellows are as of yet unaffected. Lethal, odourless chemicals are easier to get your hands on than nuclear and biological weapons and can potentially kill in a moment especially if the chemical's uptake is accelerated.

Tie their shoe laces together?

In all seriousness, your best bet is to use their speed against them. It doesn’t matter how fast they’re running, if they fall over they won’t be running for much longer.

By far the simplest way of stopping them is to dig a 1ft by 1ft by 1ft hole, essentially a rabbit hole. If you’ve ever stepped in one, you’d know how easy it would be to twist or break your ankle. Now, imagine you’re running at these high speeds, not a care in the world, and step into one of these holes. At best, you’ve twisted your ankle and torn the tissues in your leg, you might instead break your ankle, your leg, damage the nerves, tendons, muscles, perhaps even the artery in your leg. A potentially fatal but easy to construct trap.

Going slightly bigger and more advanced, you could have the good ol’ pit fall trap, a large pit covered by a tarp and hidden using sticks and dirt. The speedster runs over that, they’re going too fast to stop and falls in the hole. The fall may not be lethal, they may just break their legs in a cruel twist of fate, but you can easily make it lethal by putting wooden spikes at the bottom.

Further options are trip wires, caltrops, raising low-barriers or wet/slippery surfaces. All of these would cause major issues for a speedster. I also remember a story, i don't know its true though, where during the second world war, piano wire was tied to trees or lampposts so that the wire stretched across roads. This wire was tied so that, if you were sitting down, it would be at neck height. The idea of it was to kill Nazi motorcyclists by decapitating them as they drove past, using the speed of their bikes against them. Because of how thin piano wire is, you wouldn't be able to see it and, by the time you did, it would be too late to stop. As i say, i dont know if this was true, its just something i’ve heard.

Taking inspiration from that idea though, you could have walls of clear glass, like French sliding doors. If a speedster ran through it at high speeds, they might be cut to ribbons by the shards of glass and have glass in their eyes.

If you were talking about in combat though, i suggest pike formations. Speedsters, like horses, aren't stupid enough to run into this big, sharp pointy stick. However, if you had these hidden in long grass, for example, and lifted them up when they got close, they may not be able to turn back in time and be skewered.

Have the speedster depend on some rare substance that is expensive in order for their power to work.

For example, speeding up may require quicksilver, which is another name for mercury. The speedster might be able to break a thermometer and drink the mercury inside without suffering any harm, but that will only last them five deconds of real time.

If you really want to get serious, the main resource that may be consumed by speeding is lifetime. In George R. R. Martin's Wild Cards, there is a speedster who uses his powers for OP speed akin to the Flash's. After what seems like just a few minutes to him, though, he has biologically aged a handful of years. A little more usage of that power and he would drop dead of old age.

Area attack.

In non-lethal version, that can be used even in crowded space, I find some irony of trying to run using super speed while having zero visibility because of smoke cover. For extra bonus tear gas can be used.

In lethal version there is always artillery barrage or chemical weapons.

For defensive purposes, his super speed would be of limited advantage, while dealing with electric fence. But the most evil trap could be... a glass door.

I'm also curious, whether its possible to make a trap activated by Doppler radar.

I recomend looking at Wally West (Kid Flash/Flash III) rather than Barry Allen (Flash II) and Bart Allen (Kid Flash II/ Flash IV). Yes, there are four Flashes. Forget the golden age one but he's the old guy with the winged helmet. Anyway, all but Wally West were attached to something called "The Speed Force" which allowed a lot of physics defying that Wally West had to account for. Wally wasn't as fast as the other Flashes and had to count calories to an insane degree. He also could get injured from hitting something hard at speed.

Another Speedster to look at is X-Men/Avenger's Quicksilver, who was pegged closer to speed of sound than Speed of FTL that the Flashes had. Quicksilver's speed was more related to localized time distortion (very implied... it took a power boost to figure it out) and thus, he's moving at an average speed to his own point of view while everyone is going slow. To everyone else, we're moving normal and he's moving fast. This has some other weaknesses such as an inability to run across water, because he's technically not running fast enough to not break the surface tension. He's also gonna hit with the force of an enhanced human (but he can hit you many times over before you can swing back). Running into a wall or obstacle still hurts as if he had done it normally. And of course, he can't run the vertical length of a building without gravity getting the final word on him.

This is also the in comics ability of the Space Stone, (as opposed to portal generation in the films), and the first person depicted weilding it was a character called "The Runner". Here, speed is achieved by folding points in space closer to the wielder's forward motion and expanding it once the point is behind him. From an outsider's perspective, he is covering a distance of miles in the same time ordinary people can cover feet. From his own perspective, the distances is shorter... He is literally "Making the Kessel Run in 12 parsecs" fast because the Kessel Run is normally 24 parsecs or some much greater dsistance.

Since speed (v) is distance over time (v = d/t) those that have the power to manipulate either space (Distance) or Time selectively can achieve high speeds but not have to factor in limitations.

Make the speedster unable to interact with the physical world while travelling at ludicrous speeds.

While they can travel at speeds well above sound, or even possibly light, they can only do so by not being entirely in our physical universe. When the speedster phases out of the universe, they are actually running in a parallel dimension that lacks friction, relativistic constraints, etc.

However, in order to interact with our phase/dimension, he/she has to re-enter and become subject to all of the laws of physics. This can allow you as the writer some flexibility, as the speedster could time the rentry and speed changes so as to take advantage, but then it would either have to be pre-planned (ambush move) or would involve significant risk of going wrong. It would be much easier for the speedster to re-enter normal space time without interacting with anything, act, then speed off again than to attempt to do something during the transtion between the alternate state and the natural state.

Hopefully that would be limiting enough, while still allowing the speedster to be the sort of menace you want.

Kinetic-Energy reactive materials

As show in the episode "Fallout", of Season 1 of The Flash, Wade Eiling threw kinetic-energy reactive needles at The Flash, immediately incapacitating him, and nullifying him, as he dropped to the ground, in great pain, unable to move. Needles, bullets, swords, suits (for hand to hand), anything made from kinetictanium (pff!) could defeat a speedster, as they would home in on them. Not to mention traps, if one is expecting a speedster.

This is obviously not scientific, considering that I doubt such a material does exist in real life (please correct me if not), but superheroes also don't, so, you know.

Wiki link, but it has all the pretinent information. https://arrow.fandom.com/wiki/Kinetic_needles

Momentum

One of the issues with speedsters is that they appear to be impossibly fast, but also impossibly agile. Take the latter away.

Now, they can attain fantastic speeds, but once they're going it takes a hell of a lot to change course. A judiciously placed and unexpected barrier could see the speedster paste themselves over a considerable distance.

Computer-controlled autonomous weapon systems.

Link a weapon system to a computer system and sensor array which is able to detect speedsters and automatically fire the weapon.

Can the speedsters outrun a hypersonic homing missile?

If they can, can they outrun a hypersonic railgun?

Even if they can, they certainly can't outrun a laser beam.

You can also make it very human or real, for example they have the reflexes of a cat and speed of a Cheetah. So he caps out at 60-70 MPH / 90-110 KPH. But can only do that for short sprints, and the nemesis could be a satyr that can consistently run at 30 MPH or 45 KPH for much longer periods of time. Those should be humanly achievable with slight genetic changes, but not world breaking like running back in time. A formidable person/chimera, with clear limitations and strengths and wall running.

Give them meaningful restrictions. Personality flaws can be that, but sometimes that comes off as bad or worse, unfun, writing. A character too stupid to abuse an obviously overpowered ability like superspeed can break immersion and put off the audience. Physical weaknesses are preferable because they're easy to visualize and harder to bend for the writer. Kryptonite-like substances are a simple, but somewhat overdone, solution.

I would suggest trying to put a "spin" on every power, some in-built mechanical hard limitation. What if the speedster draws his power from making his own body lighter? He could move very fast, but his attacks would not do much damage. Or he can no longer see and hear once he passes a certain treshold of speed. Maybe he doesn't move much faster than a normal human at all, but can accelerate to his top speed instantly, which would still allow him to attack at blinding speeds without making him as overpowered as a general purpose speedster.

The trick to taking out a speedster is to present a threat that he can't understand until it's too late.

In one of the Teen Titan comics Kid Flash is taken out by poisoning the room. The poison is mostly harmless to everyone else because they inhale it in small doses, while Kid Flash breaths in so much of it fighting them quickly that he falls unconscious.

Contact poison or even something that has to enter the blood stream could work well. There are substances that will seep through skin, and even most gloves and are almost instantly fatal. No amount of speed will warn you not to touch the doorknob. You simply must set up a situation where you can manipulate a speedster to follow a certain predictable course of action, like opening a door to save someone from a burning building.

And if all that fails, just shoot him when he is not looking. Bullets are supersonic, and should give no warning no matter how fast you are if you can't see them.