That's fine. My idea is actually kinda far fetched but easily toned down.

I have made a Clone Unit known as the 117th Attack Battalion. The idea is that when Order 66 came down, they 117th were out of communications range, and thus never received the order. Through other means the Jedi General, Jedi Knight Kelen Rolin, learned about what had happened (The Destruction of the Jedi Order, The Betrayal of the Clones, the Rise of the Empire, etc...). However, instead of trying to escape his clones, he decided to help them, and ordered the removal of the inhibitor chips from all his men.

He kept his force on the fringe of the known galaxy, knowing that they would eventually be hunted down if discovered. He believed that until a significant opponent of the Empire emerged, any offensive he made would be taken out. Years later, he would hear news that a group known as the Alliance to Restore the Republic, or Rebel Alliance, had destroyed a massive Imperial Superweapon, the Death Star. There was his possible ally.

Not wanting to risk revealing his full numbers yet, he took his Padawan, Twilek Jedi Padawan Teela Kamara, his Clone Commander CC-7501 "Bronze", and the groups most elite unit known as Hailfire Squad, and headed into the galaxy to search out this Rebellion. Eventually, he happened upon Ord Taranos, which had a strong Imperial presence in the system but was also home to a Rebel Cell. Not the easiest group to find, even harder to meet given the circumstances. While he searched for them, he made life... difficult... for the Imperials, as he began nicking away at their numbers.

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This is the summary of the idea I had. If it doesn't work, I've got another continuity I could use, but not many have actually considered something like this, an entire Clone Battalion who never received Order 66, and ended up fighting against the Empire at some point.

At most, I can delete the rest of the Clone Forces, leaving just the Jedi, Commander, and Hailfire Squad as the Rogues.