Quick. Think of a ninja. If you imagined them as an honorable Feudal-Japanese assassin dressed entirely in black and throwing shuriken at their enemies, I've got some bad news for you.
This isn't to say that they weren't bad asses in their own right. They were definitely real and they definitely did many high-profile assassinations that continue to astound the world hundreds of years later. They just didn't do things the way films, video games, and literature (in both the West and Japanese pop culture) depict them.
Much of their history is often shrouded in both mystery and myth, making actual facts about them sketchy at best and inaccurate at worst. What we do know about them comes from either the most high-profile, like Hattori Hanzo, or the very few verified sources.
1. They were never called "ninjas" in their time
The term "ninja" is actually a misreading of the Kanji for "Shinobi no Mono" or "the hidden person." This was shortened when their legends grew to just "Shinobi" or "the hidden."
"Ninja" became the more popular name for them after WWII for Westerners who found the word easier to pronounce than the actual name for them. Ninja eventually circled back and became the more used term in Japanese culture as well.
On a related note: This is also how the term "kunoichi" or "Female Shinobi" came about. There may not be historical evidence of women acting as deadly shinobi, but they could have been used for other ninja tasks. Which leads us to...
2. They would scout and collect intel more than kill
There were many tasks of a Shinobi. It is well-documented that high-ranking leaders hired Shinobi to assassinate their enemies, like Oda Nobunaga and everyone who tried to kill Nobunaga. But the most useful Shinobi were "monomi" or "ones who see."
Their espionage skills were so revered that it's said even Sun Tsu wrote about them in Art of War. Monomi would either hide in crowds or sneak into a meeting so they could eavesdrop on important conversations. Once they learned what they needed to know, they'd get out of there.
3. They never wore the all-black uniform
To nearly every other fighter in the history of war, a uniform has been an advantage. Shinobi, like everyone else doing undercover work in plain sight, would be stupid to wear anything that screams out "Hey everyone! I'm not actually a monk. I'm a deadly assassin!" They wore whatever they need to to fit in.
The uniform that everyone thinks of comes from kabuki theater. The crew who would work behind the stage dressed in the all-black uniforms to not distract from the performance while they were rearranging the sets or setting off the special effects. Fans in attendance would occasionally catch a glimpse of a stage hand and joke that they were shinobi. The "joke" part gained momentum and it just sort of stuck.
4. They used everything for weapons except throwing stars
Let's be honest. Throwing stars aren't that deadly? It's just a sharp piece of metal. Want to know what they actually used? Bows, poison, primitive flamethrowers, and damn near everything else. This includes the least stealthy weapon in feudal Japan, guns.
They did use their iconic swords, but the most common weapon was an inconspicuous farming sickle attached to a chain. After Oda Nobunaga tried to ban swords in Japan, no one cared if a farmer still had a sharpened sickle, so it wouldn't seem out of place.