Yoda sat in a meditative state in the swamp of Dagobah as he had used the force to see what had went down on Malachor, he couldn't be more disappointed.
Kanan Jarrus, formerly Caleb Dume, was blind, Maul had escaped the planet, Darth Vader was still alive, and Ezra Bridger was beginning to fall to the dark side.
But he took some comfort to know The Empire's best inquisitors had fallen on the war-torn planet.
And also, Ahsoka Tano, his greatest threat to Luke Skywalker's eventual training, was trapped on said planet.
It wasn't the fact he didn't like Ahsoka, no, he viewed her as a threat to the plan Obi-Wan and him had set up Fifteen Years ago after the fall of the Jedi and The Republic, if Ahsoka was to meet Luke, she would teach him to be just like her fallen master and threaten the future of the Galaxy and The Jedi's eventual return.
So, when Ezra had contacted him again in the Lothal Jedi Temple, he had devised the plan to eliminate all the factors that threatened The Return of the Jedi. The Jedi Code was clear and all three, Kanan, Ahsoka, and Ezra, had all broken it.
Kanan, formerly Caleb Dume, had violated the attachment rule by entering a relationship with the Twi'lek pilot, Hera was it?
Ezra was much like Anakin, he was brash, occasionally arrogant, guided by his emotions instead of Reason, and his future was clouded. He would definitely sway Luke off the correct path if he was to meet him.
Ahsoka Tano, she was the greatest threat of them all, she was too much like her former master, Anakin Skywalker, she would teach Luke everything that went against the Code and The Order, plus, she had left the Order and defied everything that was taught to her, she was to be the instrument that would make Anakin a more responsible Jedi, but instead they had gotten close during the Clone Wars and made each further defy the Order.
Yoda knew about what was in wait for them.
He knew about Maul and The Inquisitors being on the planet.
He knew that the presence of more Jedi, especially Ahsoka, would draw the presence The Order's greatest failiure.
Did he feel guilt for what he had done, yes, but he believed it was a necessary evil to do what was best for the return of the Jedi Order.
But now, the plan had only somewhat gotten his results, but now it seemed Ezra and Kanan would have to remain to hold off The Emperor, Vader and Maul till Luke was ready to be trained.
For now, he would wait, plan, and prepare for the eventual revival of The Jedi Order.
I had a PM chat with another user a few days regarding 'The Shroud of Darkness' and 'Twilight of The Apprentice' and I came up with a VERY long, stretchable theory regarding what went down.
What if, when you think about it, you think about all parties, Anakin/Vader Ahsoka, Ezra, and Kanan have defied the Old Order which Yoda speaks highly about, if he's been watching the galaxy through the force in his exile, he may trying to weed out those who he thinks will lead the new order to ruin with different ideals and he attempted to teach Luke to his way of thinking.
If this theory is true, it would make Yoda just as vile as Emperor Palpatine.
Me and this certain user, who writes a certain Shaak Ti is Ahsoka's Mother and Redemption of an old Order stories, have believed that over time from The Jedi's founding, they had become increasingly corrupt and rigid with the Jedi Code, losing sight of compassion and emotion.
They've been corrupt till the end of the Old Order, who's to say Yoda is also among them.
So I made this to explore what was going through Yoda's mind in the events of Malachor if this theory was to proven true.