"Dooku was right in the end. He knew the Republic was corrupt, that it would collapse and become something worse. He saw it coming. The Galactic Empire." -Tawni Ames
(This is NOT a Dooku defense post.)
Poor Cody was really going through it in "The Solitary Clone". He's questioning everything but he feels so alone because the internal conflict he's experiencing isn't something he can openly and safely express in this new Empire he's serving. He's feeling immense guilt over Order 66 and has to hide it, to bury it down deep, and he pushes on because he doesn't know what else to do. He was hoping Crosshair would be different, but it turns out Crosshair is still willing to commit murder for the Empire.
What I love about this episode is the way that it humanizes the Separatists. And no, I'm not legitimizing Dooku or General Grievous or any of the other horrible war criminals serving in the Separatist military. I'm talking about normal, everyday people trying to live their lives. They weren't bad. They weren't stupid. They were deceived, but so was the Republic. The Republic was literally serving the whims of a Sith master and didn't know it. There was no real legitimacy to the Separatist movement because it was being spear-headed by a Sith apprentice. Palpatine and Dooku were in it together and managed to deceive an entire galaxy into division.
Dooku was right because Dooku was helping create the conditions that would allow the Empire to rise. The Separatists have no idea that Dooku was in on it (and never got to find out because Dooku was executed by Anakin on the orders of Palpatine, who wanted to make sure that his co-conspirator was silenced). Dooku being right certainly didn't give him the moral high ground considering he was rigging the game, but the truth behind everything was hidden away.
"Peace? There was a time I believed in that. So much so, my colleague Mina Bonteri and I put forth a treaty with Separatists and Republic senators alike to end the war. Your Supreme Chancellor rejected it. I realized then, peace was never an option." -Tawni Ames
At the end of the day, both sides wanted the same thing, but they were blinded by lies, propaganda and fear. "The death of truth is the ultimate victory of evil" was happening long before Mon Mothma ever spoke those words to an Imperial senate.
Commander Cody: Listen, we both lived through one war. Let’s not start another. Too many people have died already. We can resolve this without more bloodshed. Please, do this for your people.
(Tawni lets go of Grotton)
Governor Grotton: Nicely handled. Now execute her.
Commander Cody: Sir, I promised a peaceful…
Governor Grotton: You did. I didn’t. Now execute her!
Tawni Ames: So much for peace.
Cody listens to Tawni Ames though. He understands her side a little more now. The truth of what happened isn't uncovered, but Cody chooses peace in that moment. He understands that the truth is a lot more complicated than he once thought. He doesn't want to solve the problem violently, wants to give her the chance to speak, is extending an olive branch, and refuses to obey when ordered to shoot her. He was trying to save her life, but Crosshair shot her down instead.
He was confronted head-on with exactly what the Empire was in that moment. This is most certainly not what he'd been fighting for during the Clone Wars. The Empire rose at the cost of the Jedi Order, and Cody was the one who had commanded the 212th to turn on General Kenobi. The weight of his guilt must be heavy because he knows he made a mistake and it's one he can never apologize for because he believes that Obi-Wan is dead. He tried to do the right thing on Desix, tried to negotiate, but the Empire would rather kill than negotiate with anyone who challenged their authority. All the Empire cared about was domination by any means necessary.
The clones were the ones who helped usher this in (the vast majority of them not realizing they'd been programmed), and there was no way to undo the damage being done. Cody could no longer be a part of it though, and he defected quietly, alone, and with no clear path ahead of him.
I hope we eventually get to find out what became of him after this episode.