
Stephanie C. answered 06/19/19
English BA, copy editor and proofreader can improve your writing!
Every ability has inherent weaknesses, more so if it is extreme. Are you positive your overpowered antagonist has no flaws or weaknesses? Often the greatest strength is the biggest blind spot. Perhaps your antagonist has a weak spot you've overlooked. There's always good old hubris and overconfidence.
The way you phrased your questions puts me in mind of game character design in the way that powers and abilities must be balanced. For example, you can have a character who is extremely physically strong, but then they are usually slower and less agile. This leaves them vulnerable to a quick or sneaky character attacking from behind or something like that.
Or in terms of non-physical abilities, if you design a magic user, they might have super effective offensive spells but have little defense against just getting punched in the face. And maybe their super spell can only be used once, so if they miss they're vulnerable to a counter-attack.
Even gods of the Greek pantheon had plenty of flaws and weaknesses. Is your character really totally invulnerable? Clever humans were often able to prevail against the Olympians.
Or look at Achilles, one of the most famous literary characters whose major quality was being nearly unstoppable, but he was ultimately all too human.
A different angle you might consider is shifting the conditions of victory or defeat. Most situations are not simply a zero sum game with finite options.
Sometimes you win by delaying until something changes in the world, like stalling until nightfall or an eclipse or the arrival of an ally.
Sometimes you win by refusing to engage an enemy directly and wasting their resources and time in a war of attrition.
Maybe it's impossible to win except by cheating, like the famous example from Star Trek, the Kobayashi Maru.
Maybe the protagonist has to step outside the conventional set of possible actions, like the giant's drink game from Ender's Game (novel by Orson Scott Card) in which choosing either of two options presented by an adversary ends in death, so the protagonist "breaks the game" by creating a third option no one ever considered.
Either that or you've written yourself into a corner and it's time for major rewrites. Or turn the story into a series. Failures leave room for comebacks. There's always a tomorrow as long as your protagonist isn't dead, and sometimes death isn't permanent or a new protagonist picks up the story and keeps going.