The Clone Wars was a dark time in the Star Wars universe. With the stellar conclusion of the animated series, certain questions came to mind once again. These aren’t necessarily new questions, and they may have been answered in a random novel, comic, or encyclopedia I just never came across. There may not be an actual answer, but it’s something that really got me thinking during the last few episodes of the series.
What did the Jedi Council have planned for the clone troopers when the war was over?

We know it was Jedi Master Sifo-Dyas who knew a war was coming, and the Republic would need a clone army. The Jedi did not agree and had him removed from the Jedi Council. Despite this, he secretly commissioned the Kaminoans to get things started. He was ordered killed by Darth Tyranus/Count Dooku, who obviously was working under orders from Palpatine. Palpatine took over Sifo-Dyas’ idea for his own masterplan.
When Obi-Wan Kenobi discovered the creation of the clones, the Jedi Council and Supreme Chancellor Palpatine decided to use them for the war against the Separatists. Whether or not the Jedi Council was able to foresee the outcome of the war, they must have given some thought to what would happen to the clones regardless which side won.

Part of the Jedi code is compassion for all lifeforms. Since the clones were created, perhaps they were just seen as a tool or weapon in trying to win the war and protect countless lives within the Republic. Did they simply view clones as objects to use like droids or weapons?
The clones may have been accelerated in their creation, but they were alive. This would mean they would have some sort of rights under the Jedi’s point of view. Throughout The Clone Wars, we’ve even seen the troopers take on distinct traits from one another and adopt individual names. When Commander Rex talked to Ahsoka about the war, he mentioned many of the clones were conflicted over it.

Were the Jedi mindful of this self-awareness on the clones’ part? The Jedi likely believed they would inevitably win the war. Did they have plans in motion to allow the troopers to retire and live wherever they wanted on some sort of pension? With the immense number of clones created and the new batches created towards the end of the war, where would all this money come from? Would they have to fend for themselves to find a job or dwelling to live?
Maybe the Jedi would encourage them to continue serving the Republic to help keep the peace. They may have had a shorter period they could actively serve due to their accelerated growth, but they would still need somewhere to go after the war. Would the Jedi simply abandoned them as they would a derelict starfighter that was longer needed? Could it be possible the Jedi didn’t see them as having rights and had some horrific way to permanently retire them?
The Jedi may come across as big jerks from time to time, but that sense of compassion does exist within them. We have to believe they would do their best to ensure the clones would somehow live the rest of their artificially created lives comfortably. They may not have approved their creation in the first place, but did see and take advantage of their value when they were discovered. They were taken care of and respected by the Jedi generals who led them in the various battles.

Whatever the case, we may not know what ultimate plans the Jedi may have had (unless, mentioned, it was revealed at some point and I simply missed it). We’d have to assume they probably would have had a better life than what they had serving under the Empire. It’s likely they were utilized and converted into Stormtroopers and dump at the first sign of being incapable of serving. The troopers may have had Order 66 added to their control chips, but they were the real heroes of the war…as long as you overlook that awkward Order 66 fiasco.
