The talks
Captain Rex was just explaining all this (the prologue, which to those who did not read it is just what happened in the first couple of episodes in Season 6 up till the part where Fives discovers the implant in Tup's brain) to Fox(a clone trooper). He was saying, "Now I want you to tell me what happened next."
"How d'you expect me to know?"
"You, my friend were given the order to kill Fives."
"I admit that. But that and what you are telling me are two completely different things. Your story is unbelievably crazy. And I would like you to tell me how you even found that out."
Rex smiled. He knew that Fox had also been investigating about the case. Rex himself had found out about it from the robot that was in the hospital and had helped Fives. He said, "That is a small matter. Leave my story out of this. Just tell me what happened that night."
Fox sighed. "Fives had become rogue and so I was given orders from Chancellor Palpatine to hunt him down and kill him. I followed my orders. That's it."
Rex tried to connect the dots. A thought was coming to him. He thought that he should think about it later. He had already revealed too much to Fox and he had a bad feeling about that. So he said, "Thank you for spending your time with me Fox."
"As always, it is an honor" said Fox though Rex thought he could sense a slight sense of arrogance and jealousy in his voice. This confused Rex because those two feelings usually did not go hand in hand. But then again these feelings would fit perfectly in Rex's still forming conspiracy theory.
Rex thought to himself, "What if the Chancellor was the conspirator i.e. what if he wanted to hide the fact that there was an implant in Tup's brain? And for what reason? Did he plant it there?" Then Rex started cursing himself for revealing the information to Fox. He could be an agent of the Chancellor. That would reason for the arrogance in his voice and his jealousy could be reasoned to Rex's position. Rex already had made up his mind that the Chancellor had planted the implant in Tup's brain and now Rex had another thought.
He scanned his brain the next day and he found that the same implant was there in his brain. He thought to himself, "Why didn't any clone ever scan their brain? This chip must be there in all of our brains! Now why did the Chancellor do this? I cannot risk telling this to anyone else however."
Fox had right away gone to the Chancellor after the meeting and reported what had happened to Palpatine. Palpatine said, "Though we recognize the great capabilities of Captain Rex he has turned into a menace. Arrest him and bring him to me for questioning. And don't breathe a word of this to everyone or else there will be pandemonium in the streets. And we certainly cannot afford that. Now go and take with you a squadron of men."
Meanwhile in the Jedi Council Ahsoka Tano was exiled.