bjornwilde

Thinking out loud here since I mentioned this to Cam...the basic plan is to save Captain Rex from Order 66.

What we know:
Ahsoka is not a part of the Jedi Order when Order 66 occurs.
Captain Rex gives up his command or is replaced before Order 66 and the attack on the Jedi Temple occurs. It could be anywhere from a few months to a year before Order 66, Wookiepedia just lists 19BBY whereas Order 66 took place in 20BBY.
I, as yet, cannot find a reason for him giving up command.
Before he gives up his command, he and Anakin nearly capture 5s, another clone trooper who's discovered the organic chip, implanted at birth, that causes the clones to attack jedi. 5s is framed for attempted assassination of Palpatine and ends up being killed. As he is dying, 5s rants to Rex about the chip. His "malfunction" is excused as a rare brain parasite.

Headcanon, or what I am planning:
Rex leaves the 501st due to unease with how things are going. He's losing faith in the Republic. He still loves his brothers enough to know his doubts put them in danger and so he relinquishes his command.

Free of duty for the first time in his life, he decides to go in search of Ahsoka. Alternatively, Anakin asks him to give up his command so that he can go in search of Ahsoka. This second option seems to fit Rex's adherence to command structure more.

Rex has trouble finding Ahsoka and ends up taking the rest of the war to get close. At some point, he finds some clone trooper armor at a pawn shop or flee market and can't stand to see it being disrespected and so buys it. He cleans it up and gets it functional just in time for the Order 66 broadcast. Having no jedi nearby to trigger the organic chip, Rex nonetheless becomes obsessed with finding Ahsoka.

Finding her, he attacks but his behavior is very erratic; alternating between psychotic and ranting about the chip, basically giving her enough of a clue to look farther. Of course, she can't look farther while he is trying to attack her.

Enter Shephard. I figure she has sedative drugs she can give him but she can't do that and restrain him at the same time. Next step, once he is sedated, is to decide if Rex goes to Milliways or if I see if Wedic would like to give Guppy an off world adventure. I figure the chip is small enough that a standard medical droid is not a good idea, or maybe Ahsoka's medical droid is older, if she even has a medical droid. As well, with the fall of the Republic, going to a medical facility may not be a good idea.

I like the idea of seeing if Guppy can come to the SW universe cause then I don't need to have a blank character slot needed to bring Rex to Milliways. I'm also liking the idea of Anakin giving Rex the one last order to find Ahsoka and watch her back. Kind of poetic given Anakin eventual role in the Empire.