You can have three guesses who's going to win. The first two don't count.
In any martial arts fight, there is only a finite amount of ninjutsu available to each side in a given encounter. As a result, one Ninja is a deadly threat, but an army of them are cannon fodder.
A specific form of Plot Armor, this trope is very common due to the numerous storytelling considerations fueling it. Drama thrives on conflict, and having the few put up a fight against the many is basically a free conflict coupon that's automatically viable during any few vs. many confrontation. Why have the superhero team curb stomp the villain if you can make him powerful enough to force them into Teeth-Clenched Teamwork? Why have the dozens of Mooks club The Hero unconscious three seconds into an encounter if you can let him take down seven or eight of them before he collapses, to show how much of a badass he is? That would be letting some perfectly good dramatic tension go to waste.
As the number disparity grows larger, another factor comes into play—there's strength in numbers, but also anonymity, which in fiction is a crippling weakness. Characterization is a precious, rare resource that is difficult to set up, which means most characters are not going to get any. Since characters often travel in homogeneous packs in terms of characterization depth, the larger a group is, the less characterization its members probably have.
In other words, if Team Meager is up against Team Gargantuan, we probably know something about Team Meager and at least care how well they're going to do in this fight—maybe we even outright sympathize with them and root for them to win. Team Gargantuan, on the other hand, is likely a faceless blob of Mooks or Red Shirts that we don't care about on any personal level. Letting Team Gargantuan steamroll over Team Meager in this scenario would be anticlimactic; not letting Team Gargantuan do that means playing this trope straight almost by definition. Often Team Gargantuan instead of applying their numbers, tends to get in line waiting to get beat in turn.
Hence, you end up with the few gaining an almost-automatic boost to their capabilities when pitted against the many. Extra points if, when presented with their multiple adversaries, one character notes that "We barely were able to handle one, how on earth are we going to handle this many?" right before successfully doing just that.
This can, of course, apply to Elite Mooks other than ninjas. Vampires are particularly susceptible to Conservation of Ninjutsu, as are werewolves, alien monsters, Special Forces commandos and Super-Powered Robot Meter Maids.
There are a few conceivable ways in which this trope can be Justified:
- The most obvious one is adhering to Magic A Is Magic A—if you consistently portray someone as powerful enough to take on a large number of people by their own and put an explicit limit on what they can and can't do, the Willing Suspension of Disbelief will not suffer nearly as much. How to establish the superiority of small numbers in concrete terms is another issue.
- Another is to introduce some superior technology or art, available to the small group but not the larger group, that evens the odds (think the armies of Saladin vs. an M1 Abrams Tank). If stealth specialists are forced to fight head-on heavy hitters who excel exactly at this job—which is usually the case with the "ninja" form of the trope—it's a bad strategy, and heavy losses are expectable, too.
- One more plausible scenario for this trope is if a smaller group of people is simply better coordinated than a larger group of opponents, and tries to stack the odds in their favour, however they can—cutting off paths for reinforcements, luring enemies into ambushes or traps, or disrupting their communications. This relies heavily on the element of surprise, as well as considerable planning and ability to adapt to situations on the fly, and would be considerably more effective if the group had some of the previously-mentioned advantages. In any case, if the element of surprise is lost or if the plan starts to fall apart, you can expect things to get very bad.
Examples
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