There are a few misconceptions here and I would like to address to
(relying only on my knowledge about ninjas, so it could be all wrong if riot wants to)
Anyway, here are some points people seem to be making:
1 - Shen's father died on his trial to test Shen, not by Zed's hands
That is not very true, Shen's lore states that:
|As his final trial to ascend to this position, he was made to attend the Takanu, a ceremony in which his father was tortured before his eyes to test his resolve. Any reaction whatsoever would have resulted in his immediate disqualification, but he never averted his gaze and never blinked, not once.|
Shen's father was the master of the clan, he was prepared to endure any torture,
and his self torture was needed to test if Shen was ready for anything that could come
(and I am certain, he knew exactly what would happen)
2 - The master wouldn't simply ban a student
3 - The 'evil box' sounds like a silly idea
That's all in the balance.
Shen's clan lives to preserve the balance.
There is no balance without evil
The master trained 2 pupils, One to be the "good" and other to be the "evil"
He NEEDED that to preserve balance.
He knew that banishing Zed would make him become an evil master of shadows,
while Shen was always destined to be the Eye of Twilight.
The box, is what is commonly known as "Sealed evil in a can".
The Evil cannot be destroyed, to preserve balance, it needs to exist. So they seal it in the box, to make sure it exists, while it cannot do any evil things that aren't planned
(unless he manages to escape the box, then ohh boy we are all doomed)
Shen's father, he did that to Zed to preserve balance, an enemy to Shen must exist, and he needs to truly be an enemy, not just a rival.
4 - Why would the master simply allow Zed to enter back?
5 - Why Zed would scream in pain while inside the clan?
That's pretty simple.
It was all staged.
Shen's father staged it all, he knew what would happen and it was needed to happen.
Zed had trained his soldiers but he simply had no purpose other than get stronger.
He needed to transcend to the real evil master of shadows, to preserve balance, since Shen had reached the point of being Eye of twilight.
He waited for Zed's return.
Staged the "I failed as a master, come and destroy the box".
Zed was confused. he was ready to kill his former master if needed, but he would never kill him without a reason. A true evil master of shadows should not hesitate to kill his own master, however, that's what was separating the Zed walking into his old temple, from the Master of Shadows Zed he needed to become.
He enters the temple, go to the box.
There he is not sure what to do: Steal the box and be master of his own clan?
or destroy the box and join his former clan?
He does have a doubt. He cannot have one however, Shen's father must assure he will choose the path of darkness and transcend to a new level.
So he back stabs Zed. Zed was taken by surprise, but then he realizes it was all a trap to kill him (not exactly, but staged to make look like it).
He angers himself, and in his almost infinite wrath, he kills his master and anyone else in his way.
He claims the temple for himself, and as a master of the new temple and new clan, he finally became the evil master of shadows he was destined to be.
There are no inconsistencies. It all works the way it needs to be to balance be preserved.
Some of you underestimate the power and knowledge to a clan's master.
He did his job, which included send one of his pupils to light and other to the shadows.
It included self torture to test the chosen of light, and ultimately, his death by the hands of the chosen of darkness.
After all, he toyed with his destiny, he deserved to die to make it fair.