Zed and the Nature of Shadows
Anyone who has given lore a cursory glance likely knows that Zed is a ninja that employs forbidden techniques to assassinate his targets. This particular method of killing is done with the assistance of shadows, copies of the user that are every bit as dark an indistinct as the title implies. However, even the most thorough investigation reveals little to nothing about the shadows. In fact, few people even seem to question the nature of Zed's technique, or draw any attention to it at all.
I feel there is something suspicious at work concerning the Shadows, something sinister hiding in plain sight far more dangerous than one upstart ninja. There is a reason the knowledge of Shadows was locked deep within the Kinkou temple, there is a reason the technique is forbidden, and there is a reason Zed's master, Shen's father, wanted to end it's continued presence.
Warning: the following is entirely my speculation.
It Starts With A Seed
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Zed was the first ninja in over 200 years to use the power of Shadows, the first to venture deep within the Kinkou temple and open a box of forbidden knowledge. Just a peek, but it was enough to give him an edge over his then peer Shen. For his audacity, Zed was banished. That seems a bit harsh for the nature of his challenge to Shen; they were not fighting for a position of authority or on behalf of the Kinkou, it was an entirely personal matter, the only ones who would be affected were Zed, Shen, and their mutual master.
Why would Zed be banished without question or hesitation? Admittedly, Zed essentially broke the rules of the Kinkou Order, and rules are a serious issue for ninjas; if you cannot be trusted to follow rules, how can you be relied upon by your fellow clan? However, Zed's mistake went well beyond cheating. The box he opened was buried deep within the temple, without a doubt it was locked in some manner, perhaps not physically but in a way that contains something decidedly not physical.
Ionia is a fairly mystical place, and quite old as well. Scattered across the island nation are objects, relics of the distant past, shrines of ancient purpose, all manner of things most of modern Runeterra has forgotten or simply cannot understand. As shown in Bard: Mountain, some of these items are incredibly powerful, but perhaps something that can be held is not the only vessels of power. We know that Ionia celebrates a festival where once Akali and Shen performed and ancient tale of a haunting spirit, a terrible entity that pursued its victim for years before being turned away. Not only that, but Ionia is the origin of League's own Nine-tailed fox, a former fox spirit turned - partially - human. Suffice to say, spirits exist, though not with an entirely hostile agenda.
What if the box Zed discovered contained far more than knowledge alone? He peeked inside, and his mind was touched, information imparted, not learned or taught, but implanted. However, the process was incomplete, and it would be years before Zed unveiled the Shadows' true potential.
And Then It Grows
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When Zed was banished, he took to wandering Ionia, and as he did others began to follow him. Perhaps they saw him as curiosity, maybe some were interested in the techniques he used, whatever the case may be, Zed acquired apprentices that were trained as he was. Eventually, the number of willing advocates became so large there were enough to rival an entire clan. And it was then Zed decided to return to his master, to display what he had done. In response, Zed's former master calmly laid down a sword at his once student's feet and welcomed him inside the temple.
While there is little information as to why Zed's master did what he did, I believe he understood the gravity of the situation and endeavored to handle it calmly as he could. At that time, Shen was The Eye of Twilight, a position formerly held by his father, and thus the analytical, stoic evaluation still influenced the master's actions. He realized that his decision to banish Zed had not worked out at all, as now there were many who practiced the same forbidden techniques. The knowledge had spread, and if action was not taken, would continue to spread. Thus, the master asked Zed to join him inside, destroy the box, and turn away from the shadows.
What happened exactly is a mystery, but I like to believe the master was a man who did not accept loss, not when so much was at stake; the Shadows had grown, and if left on their own, as he once regrettably allowed, would cover Ionia in darkness. He asked Zed to destroy the box, but I doubt Zed would. Years on his own, training both himself and followers, were simply too much to turn away from. He intended to open the box, and the master had planned for this as well. He intended to kill Zed, cut off the head and let the body that had become the Order of Shadows wither away. When Zed opened the box, and the last of the secret arts were revealed to him, his master struck. But something spoke to Zed, warned him of his master's grim duty, and Zed struck back. Something wanted Zed alive, to continue his teachings, something that had invested far too much in the now Master of Shadows to simply let it all go to waste.
Until it Grows Out of Control
The Shadows are alive, perhaps not as multiple entities, but as an individual, a source of terrible knowledge, and as that knowledge spreads, so too does its power. The Shadows are a spirit, an ancient evil, a darkness locked away for many years. Through Zed it has found release, not entirely perhaps, but just enough to slowly corrupt Ionia one soul at a time. Though Zed and his followers wield the Shadows, their technique cuts both ways: the Shadows wield them.
The greatest evil is one that none realize was there at all.