The entire Jedi Order was brought down by a single command by Palpatine, when he issued
order 66 to all of his clone troopers to betray their Jedi leaders.
But not all Clones obeyed.
In Canon, the clones had inhibitor chips in them which forced them to mindlessly obey
order 66.
It’s also implied that these same chips helped them cope with the fact they they just
executed their long time comrades, and possibly even close friends.
We know of only 3 clones who removed these chips, with them being Captain Rex, Commander
Wolffe, and Commando Gregor.
Although we don’t exactly know when Wolffe and Gregor removed their chips, we do know
Rex removed his before order 66 was issued.
When order 66 was given, Rex helped Ahsoka escape, and they later faked their deaths
before splitting up and departing to live in exile.
Rex eventually met up with Gregor and Wolffe, where they ended up living inside a modified
AT-TE walker on Seelos.
They were later visited by the Ghost Crew, whom would ask for their assistance to fight
the Empire.
Initially the clones refused, but after having a skirmish with the Empire and having their
home, the AT-TE, destroyed, Rex decided to join the Rebels.
While Wolffe and Gregor stayed behind and took the remaining AT-AT and transformed it
into their new home.
Then we have commander Grey.
Although he did initially obey order 66, he did finally come around and began to question
what he had done.
This later led him to sacrifice himself by betraying his clone comrades and saving a
Jedi padawan named Caleb Dume, whom would later change his name and become Kanan Jarrus.
Last we have clone medic Kix.
After witnessing Tup kill Jedi Master Tiplar, he was later confronted by Fives and was told
of the conspiracy of a plot to kill the Jedi before being asked to contact Anakin and Rex
and have them privately meet with him.
This contact with Fives led Kix to have his own questions on the matter, leading him to
investigate himself.
His investigation eventually led him to discover the truth behind the biochips and the plot
to destroy the Jedi.
But before he got a chance to tell the Jedi, he was kidnapped by the Separatists who placed
him in a stasis pod for safe keeping before delivering him to Count Dooku.
As the ship was transporting Kix, it got attacked by Republic forces.
Desperate to not have Kix fall into the hands of the Republic, the droids on the ship decided
to jump to a random coordinate in hyperspace in an attempt to escape.
When they came out of hyperspace, they crashed landed onto a desert planet.
Overtime, the droids ran out of power and shutdown, leaving Kix alone frozen within
the stasis pod.
50 years later, and Kix was discovered by Sidon Ithano and his pirate crew.
They released him from his stasis pod, to which Kix started to ramble about the sith
plot to destroy the Jedi and how he needed to get back to Anakin Skywalker and the Republic.
As this was happening, the ship they were in activated its remaining security defenses
and the pirates were forced to escape the wreckage.
After escaping, the pirates told Kix of how there was no longer a Republic and then explained
to him of what had happened in the past 50 years.
Sadden over the fact of not being able to save the Republic and the Jedi, Kix eventually
joined Ithano’s pirate gang and helped them search treasure across the galaxy.
From what we know, he is the last surviving Jango Fett clone in the galaxy.
And before we move onto Legends, we can safely assume that all clone deserters, like Cut
Lawquane, didn’t obey order 66, simply because they never received it.
In Legends, the Clones didn’t have an inhibitor chip that forced them to comply to order 66,
instead they were engineered to be dependent to a command structure and were basically
brainwashed into being loyal to the republic.
The first known clone to disobey order 66 is HOB-147.
He was a clone pilot who flew a V-19 Torrent starfighter for Light Brigade Division.
During a space battle, he was shot down and went unconscious, and he drifted in space
within his starfighter.
He was unconscious for several weeks and missed order 66 when it was issued.
He and his ship were later salvaged by Hurd Coyle, a scavenger who used reprogrammed separatist
battle droids to help him around.
When Hob-147 finally came to, he was told of order 66 by Coyle.
Initially the clone believed he was captured by a separatist, after witnessing the battle
droids.
After attacking the battle droids, he was tased and placed into a holding cell.
While in his cell, a Jedi padawan snuck in and mocked him, but she was quickly taken
away from him by Coyle and placed back into a storage room.
Witnessing this, Hob-147 believed the scavenger was kidnapping Jedi padawans.
This propelled him to break out of his chain and to find them.
He eventually discovered the 11 Jedi padawans hiding in the ship's storage room, all of
whom attacked him after spotting him.
But they stopped after seeing that he wasn’t being hostile to them, and they later explained
to him of what had happened.
While this was happening, Coyle’s ship was contacted by a group of clones who were inspecting
suspicious cargo ships for possible smuggled Jedi.
But before the boarded clones got a chance to search his ship, Hob-147 came in for the
rescue and told them about how Coyle saved him and that he had already searched the entire
ship and found no Jedi.
They believed him and left.
It’s unknown what happened to Hob-147 afterwards.
Next we have ABLE-1707, also simply known as Able.
He served under Shaak Ti during the clone wars.
During one of his missions, he was shot down and was eventually left stranded on an uninhabitable
planet after his comrades were killed around him in battle.
With no way of contacting the outside galaxy, he was forced to survive on his own for the
next 20 years.
It wouldn’t be until after the Battle of Yavin, that he would finally make contact
with other people.
A skirmish between the Rebels and the Empire took place on his planet near his campsite.
Believing the stormtroopers to be clones in new armor, he ran to them in his phase 1 armor.
But the Imperial Officer believed it to be a rebel trick, so he ordered his men to fire
upon the clone.
Able was able to escape, but was left confused with why they would attack him.
He eventually ran into Luke Skywalker and Narra.
Initially puzzled at what was before them, Luke and Narra explained to the clone of what
had happened to the galaxy in the past 20 years, and how they were fighting the empire
that destroyed the Jedi.
Luke then proceed to show the clone that he was a Jedi, just like the ones Able fought
under during the clone wars.
This prompted Able to join them and help them escape the planet from the Empire.
After successfully escaping, Able decided to join the Rebel Alliance and to work within
the Alliance Intelligence Core.
The next group of clones were all Commandos, meaning they possessed a higher ability of
independent thought than regular clones, allowing them to operate away from the more standard
command structure and freely think more for themselves.
First is Omega Squad, which was an elite clone commando unit.
Members of this unit were Darman, Atin, Fi, Corr, and Niner, the leader of the squad.
When Order 66 was issued, Omega Squad did not comply as Darman, one of the commandos,
had a relationship with Jedi Knight Etain Tur-Mukan.
Omega Squad instead decided to desert the military with Kal Skirata, their Mandalorian
instructor.
However, the carefully laid plans to evacuate Coruscant were jeopardized when Tur-Mukan
was killed during a skirmish, which also left Niner injured in the process.
Afterwards, Atin and Corr were able to escape to Mandalore with Skirata, while Darman remained
with the injured Niner.
Unable to rejoin their brothers due to the establishment of the Galactic Empire, Darman
and Niner were forced to remain commandos.
They were combined with survivors of Galaar Squad, becoming Squad 40 of the 501st Legion,
where they were tasked in capturing surviving Jedi.
Next is Ion Team, which was another unit of clone commandos.
It was attached to the 22nd Air Combat Wing.
Members of this unit were Trace, Ras, an unnamed third member, and Captain Climber, the leader
of the team.
When Order 66 was issued, Ion Team refused to execute Jedi Roan Shryne, Bol Chatak, and
Olee Starstone, believing the order to be a false enemy signal.
They then saved the Jedi from being ambushed by the forces of Commander Salvo by setting
up a counter-ambush and allowing the Jedi to escape.
As a result, Darth Vader killed two members of the team, but Captain Climber and Trace
escaped into the forested hills of Murkhana.
Vader ordered his men to hunt the commandos down and return them to him alive.
After Vader decapitated Bol Chatak, a clone shock trooper informed him that the commandos
had been apprehended.
Vader then sent them to be imprisoned on Agon Nine.
Next is Ordo Skirata.
He served as an Advanced Recon Commando.
Throughout his years as a soldier, Ordo questioned his purpose and criticized the Jedi for using
a slave army to fight their war.
Over the years of the war, he became less and less loyal to the Republic and Jedi, while
spending more and more time looking for a cure to his accelerated aging.
When Order 66 was issued, he refused it.
Ordo eventually witnessed Omega Squad try to smuggle Tur-Mukan off of Coruscant, but
their plan to save her failed when they were discovered and a skirmish erupted, resulting
in Tur-Mukan’s death.
Ordo tried to revive her, but failed.
Ordo would go on to desert the military and join Clan Skirata on Mandalore.
From there, he continued his search for a cure for his accelerated aging.
Last is Alpha-26, also known as Maze.
He was an Alpha-class Advanced Recon Commando captain.
Maze was stationed on Coruscant for most of the war, assisting Jedi General Arligan Zey.
Maze developed a grudge against Ordo, after being beat up by him after he attempted to
lecture Ordo to obey Jedi Generals.
As the war progressed, Maze used his downtime to read, and developed strong opinions about
the state of the Republic.
While no fan of the political leadership under Palpatine, he thought the Jedi should not
interfere as they were not elected.
During the Great Jedi Purge, Maze returned to Special Operations Brigade headquarters
to find Ordo and General Zey talking about the events leading to the purge.
Ordo demanded to know from a wounded Zey if the Jedi did indeed try to overthrow Palpatine.
Zey admitted to as much, stating that it was his duty as Palpatine had revealed himself
to be a Sith Lord, known as Darth Sidious.
Maze wondered what the Sith were and Ordo explained that they were the exact opposite
of the Jedi.
After Ordo left, Zey would order Maze to execute him, knowing what would happen if he were
captured.
Maze did not comply and missed Zey on purpose, giving Ordo the idea that he executed Zey.
Later, Maze would contact the Skirata Clan and ask for refuge on Mandalore.