1.  Well-constructed characters generally do not need weaknesses. If you have to resort to something like a vulnerability to Kryptonite or the color yellow or whatever, it’s probably because the character is too powerful to begin with.  Something like Kryptonite is not a satisfying or particularly effective way to resolve that.  For one thing, going from “largely unchallengeable” to “helpless rag-doll” does not make for great fight scenes.  Also, relying on Kryptonite may force writers to pull goofy Kryptonite Ex Machinas where minor criminals somehow acquire rare and random substances.*

*Some Superman stories explain this by having Lex Luthor give Kryptonite out to criminal groups, but it’s incredibly rare.  Why would a random gang have a better chance of killing Superman than his own assassins?

2.  Kryptonite-style weaknesses are a bit outdated. In the past twenty or thirty years, there haven’t been many major superheroes that have been successfully introduced with a serious vulnerability to something that’s usually harmless.

3.  Rather than using something like Kryptonite to limit your protagonist, I’d recommend limiting his capabilities instead. If the character is practically indestructible and can move as fast as a space shuttle, then you practically have to pull something like Kryptonite out of a hat whenever you want to challenge him.  But the fight scenes are generally more interesting and the character will probably be more relatable if his powers are less impressive to begin with. Over the past thirty years, heroes that are merely somewhat better-than-human (like Wolverine, Batman and Spiderman) have been dominant. Heroes that are so impervious that they need a gimmick weakness have generally not fared as well.

3.1. Another approach would be making the character’s opposition more powerful. As long as the character can be challenged, it’s not a cosmic disaster if he’s essentially a demigod. (That said, unusually powerful characters do raise some obstacles for writers — for example, if you’re writing a character like Batman, you can write interesting scenes with unpowered criminals, but a character like Superman basically forces you to pull out supervillains if you want to do anything. Supervillains usually require more thought/preparation/attention than an unpowered mook would).

4.  If you’re deadset on using a vulnerability, I’d recommend using something that is usually dangerous. For example, the Martian Manhunter has sometimes been vulnerable to fire.  That is a lot less goofy than the Green Lantern’s one-time vulnerability to the color yellow or wood. Alternately, if you’d like to try something creative, I’d recommend looking at things that are plausibly dangerous for someone with his powers.  For example, someone with particularly good hearing might be sensitive to loud sounds.  Someone with psychic abilities might be vulnerable to anything that disrupts his concentration.

5. If you’re deadset on using a Kryptonite-style weakness, I’d recommend having it be merely damaging rather than incapacitating. As noted above, if the protagonist is limping around like a rag doll after getting poisoned by Kryptonite, that really limits your opportunities for fight scenes and other interesting sequences. One alternative would be having the weakness temporarily disable the character’s powers. The character would still be very vulnerable without his powers, but at least he’d be able to try to do something. (For example, you might have him fight an unpowered battle against low-level mooks or do an escape scene where he tries to get away from a superpowered villain that is far too tough for him at the moment).

Superhero teams quite often go up against a lone villain.  Realistically, the Fantastic Four (or your version thereof) should easily be able to squish Doctor Doom (or the lone villain of your choice).

But that would be boring. Here are several ways to make it seem like a lone villain actually has a chance of winning.

1. Use minions.  Technically, this is cheating, but I won’t tell if you don’t.  You can always have your heroes fight your villain, and in between hundreds of nameless, faceless villains get in the way.  The best example of this is Teenage Mutant Ninja Turtles.  Whilst they battle Shredder about 100 Foot Clan warriors usually jump in.

2. Give your heroes something else to do.  Defuse a bomb, free the hostages, stop the plane from crashing… if there is something else needing done, you can safely split your hero team, making it more plausible for your villain to win.  This also raises the excitement level by bringing in time limits.

3. Make your villain AWESOME.  What do I mean by awesome?  Simple.  Make your villain Neo from the third Matrix film, so ridiculously powerful that hundreds of Agent Smiths are required to do battle with him.  The downside to this is that when your heroes do win, it may look contrived.

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Writers sometimes add unique weaknesses to challenge their heroes or rein in heroes that have gotten overpowered. For example, Superman has kryptonite and for a while Green Lantern’s powers couldn’t affect anything yellow.  Those two feel gimmicky.  The powers don’t work on yellow? How does that work?   Why would anyone be vulnerable to his own planet?  Etc.

A better example of a unique weakness is the Martian Manhunter’s vulnerability to fire.  It doesn’t feel arbitrary that fire might damage something.  Unlike yellow or kryptonite, fire is dangerous to most living things.  Compared to kryptonite, something generic like fire has the added advantages that it’s easier to acquire and use.

Other authors sometimes use completely innocuous weaknesses, but that’s tricky and usually contrived.  Let’s say your hero is vulnerable to marshmallows.  You’d probably have to come up with a (goofy) explanation for his weakness, then show that he somehow discovers that he’s weak against them, and then show that the supervillain somehow discovers it as well.  Generally, it’s easier to work with weaknesses that are plausible and logical.  That helps you avoid relying on ridiculous contrivances to explain how the villain discovers the weakness.  (You could work something like fire into a fight scene even if the villain doesn’t know it’s his weakness.  I don’t think you could do the same for marshmallows).

I think the best weaknesses are side-effects of the hero’s strengths.  For example, a hero with supersight might be vulnerable to intense light.  Someone with superhearing might be vulnerable to loud sound.  One advantage of these weaknesses are that you can work them into secret-identity stories.  Clark Kent isn’t likely to run into kryptonite when he’s having dinner with Lois, but he might get a migraine when a jet flies overhead.  Here are some other possibilities.

• Superstrong heroes are probably too dense to have much buoyancy.  That would make it very difficult for them to fight in water– even treading would be a tremendous struggle for someone like the Hulk, let alone Ben Grimm or Slate.  If your villain needed to escape, he could take advantage of this by flooding the room with water, knowing that he will float upwards but that the hero will sink.
• Super-fast characters would create a lot of friction when they run.  A supervillain might try to take advantage of that by dousing the room with a flammable oil (so that the friction will set him on fire) or anything slippery.  However, the slippery angle has already been used fairly extensively.
• A psychic’s powers would probably require more concentration than physical powers.  A supervillain might try to take advantage of that by flooding the room with a weak tranquilizer gas to make it harder to concentrate.  Loud noises might also work.  Finally, if the villain sets distractions before his final plot is set to go off, the hero might be completely exhausted and badly in need of sleep when the final battle commences.
• Someone that wears a powersuit is probably not very dexterous or precise when he has his armor on.  A villain may be able to trick him into taking off his suit (or at least parts of it) by planting a bomb.  I doubt anyone could manually defuse a bomb with metal gloves on.  Alternately, your villain might also try using a powerful magnet to reduce his mobility or an electromagnetic pulse to fry his circuits.
• Unlike humans, most terrestrial animals cannot metabolize alcohol.  If your character is not human (like Superman), he might not be able to either.  That could easily lead to interesting social situations.  Additionally, you could probably work it in as an ingestible poison.  It would be much less incriminating to have an assassin armed with Bud-Lite than cyanide…
• Capture the hero’s girlfriend.  Add an explosive booby trap.  Voila!  Instant trap.  Ideally that will kill the hero, but the worst-case scenario is that it kills the girlfriend, leaving the hero in an emo funk for years to come.

Alternately, you can try a quirky vulnerability to Kryptonite or something else that isn’t usually dangerous.  If you’re leaning that way, please see this cautionary article.

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