Tatooine - Spirit of Fire
After about 8 hours after they removed their inhibitor chips, the clones were started to feel like themselves again. However, all of them still felt betrayed and used by the Kaminoans and especially Palpatine. Despite this, Blue Team got to work brainstorming ideas regarding how they were going to hide Fives and secretly spread the news.
Eventually they decided that they would fake their deaths with the exception of Chief seeing as he had gained a reputation of not being able to die. Chief would go back to Coruscant and say that he took Blue Team to go hunt down Fives but when they caught him there was a fight, leading to an explosion that destroyed the Spirit of Fire. Chief only survived because he was still on the ground when it happened and listened to the whole thing over the comm.
While Chief slowly spread the news through the GAR, the remainder of Blue Team would go to the abandoned Pillar of Autumn in the Dathomir system and get it back up and running again. They needed a place to live that was big enough to accommodate more clones that would later join them, or so the plan went.
Stepping out of the airlock and on to the coarse sand, Chief looked back and saluted his team who all returned the gesture. If anything, 117 had the easy part of the assignment, all he had to do was lie about Blue Team and trek about 40km through the Tatooine desert. Throwing on an old Jedi robe that he found in the Spirit, Chief started his walk across the large sand dunes.
Eventually reaching the cesspool of a city that was Mos Eisley, Chief covered his helmet with the robe's hood, not wanting to be recognized by a bounty hunter, mercenary or gangster and cause a scene. Making his way to the Republic outpost that was located on the planet, Chief walked through the door and immediately sounded an alarm. Turns out that there was a weapons scanner that detected blasters and explosives as they came through the door.
As six troopers in plain phase 2 armour stormed out with rifles in hand, Chief dropped his cloak and revealed himself. Stunned in disbelief that the legendary spartan was in their outpost, the troopers immediately lowered their rifles. "Master Chief, what can we do for you sir?"
"I need a transport back to Coruscant, my ride here didn't make it."
"Yes sir, I'll see what I can do."
Time skip
Coruscant
After catching a ride with a supply ship heading to Coruscant, Chief was immediately brought in for questioning by a whole squad of Coruscant Guard troops. After being borderline interrogated by the Chancellor, Commander Fox and a host of other military and security personnel, Chief was finally dismissed and allowed back to work. Unfortunately, seeing as he was no longer part of the Republic Security Agency or had a team with him, Chief was grounded until further notice.
Deciding to make the most of his time and start slowly spreading the information regarding the inhibitor chip, Chief went to the person that he thought would definitely want to know what's going on. If Chief had to guess, Captain Rex was either still on Ringo Vinda or was back on Coruscant. Either way, he had to get in touch with the 501st officer.
Turns out that the official story regarding Tup shooting Jedi Master Tiplar was that a rare bacteria native to Ringo Vinda contaminated his drink and that it drove him insane. The story then goes on how Fives supposedly drank from the same contaminated drink, thus driving him insane and causing him to attempt to assassinate the Chancellor. As a result, the entire 501st was placed under medical leave and scheduled to receive 'vaccines' for this supposed bacteria.
This meant that Rex was definitely on Coruscant and likely onboard the Resolute. Making his way there, Chief hopped on a gunship that took him to the shipyards and dropped him off inside the Resolute's hangar. Before he could even go looking for the clone captain, Rex was already barreling towards him, clearly pissed off and looking for answers. "Chief, you mind telling me what the hell is going on?!"
"I will brief you on everything but not now and not here. Go get Appo and Kix, meet me in your quarters, tell no-one other than those two troopers."
"Chief, you're starting to worry me now. But okay, I trust you, I'll meet you in 10 minutes."
Time skip
After waiting in Rex's quarters for 5 minutes, the door finally opened and the three troopers walked in. Sitting all of them down, Chief explained the whole story, from what really happened with Tup and how Fives uncovered the chips. Fair to say that all three of them were in disbelief, they just couldn't wrap their heads around the fact that they have been lied to this whole time and that they were created not to fight for the Republic but to die for Palpatine's end game.
When asked where Fives and the rest of Blue Team were, Chief replied by saying that they are in hiding at the moment and are setting up a location from which they can start fighting back if it ever came down to it. Getting down to business, Chief explained what was going to happen next and the stakes that were at hand.
Appo would gather all of the veteran 501st members and inform them of the chips, Kix would then perform the procedure that removed the chips, off the books of course. In the meantime, Rex would draw up and authorize scout missions and random errands for those clones that would give them a reason to leave Coruscant. Those troopers would then get on transports and head to a set of co-ordinates where Blue Team would be waiting for them.
In the meantime, Chief had to tell the other clones that he trusted and also get the message out to Blue Team that they would be getting more clones on the Pillar of Autumn. Going over the list, there was one clone who Chief had to talk to, but he was in the most dangerous place possible. Getting back on a gunship and returning to the Republic Military Complex, Chief went to look for his old ally, Captain Fordo.
Finally finding the ARC trooper in the main command room, Chief asked if he could speak privately to the trooper. Happy to see his comrade again, Fordo went with Chief into a secure briefing room with no cameras or microphones. Getting straight into it, the spartan told Fordo about all that had been revealed in the last days and what was going on. Given the circumstances, Fordo took pretty well, throwing a solid punch straight to the side of Chief's helmet, resulting in a broken arm.
"Captain, I know this seems all made up and false, but I'm telling the truth. Every clone in the entire Grand Army has one of these chips and every brother is at risk of losing everything that makes them soldiers." Chief explained, almost pleading. He needed the ARC trooper to believe him because if he didn't, he could blow up any chance that Chief, Blue Team or the 501st had of stopping Palpatine's evil plan.
With a heavy sigh, Fordo resigned and accepted the harsh reality that they had all been played for fools by Palpatine. Telling Fordo to get Thorn and go to the Resolute, Chief explained what was happening with Kix and the other medics secretly removing the chips. Agreeing to the plan and saying that he wanted to take some other ARC troopers with him, Chief couldn't say no. The more ARC troopers they had on their side, the better. From what Fordo told him, these were the troopers that remained from his original ARC-trooper batch, and were the same ones that destroyed a major artillery position during the first battle of Muunilinst before the Seppies took it back a few months later.
The same squad would then be sent to rescue a group of Jedi that had crashed on a backwater world deep within CIS controlled space. It was there that the first official engagement with General Grevious was made and Fordo had to call a retreat, saving the lives of all his men and numerous Jedi Masters and Knights. Unfortunately, as the war progressed, the squad got broken up as the ARC troopers got sent to different missions, either advanced recon, assassinations or training the next generation of specialized forces, namely the Republic Commandos and Galactic Marines. With their squad broken up, the infamous Muunilinst 10 slowly got picked apart by the droid forces, being outnumbered and outgunned at almost every battle they were on. Chief found himself gaining a renewed respect for the ARC caption that was standing in front of him. Should they have been around when Project Ares was created, they would have made excellent spartans that could have rivalled or even beat Chief's very own spartan blue team. Thanking the captain once more for his willingness to help the greater good, 117 turned to leave.
Before he departed though, Fordo told Chief that he had an assignment which could give him the opportunity to recruit another very skilled clone group to the cause. Seeing that any opportunity was a valuable one, Chief immediately accepted. Plus, it would allow him to go off world and away from Palpatine, Tarkin and anyone else that was caught up in this conspiracy. Bidding his farewells, Chief left the ARC trooper that was massaging his broken arm, probably thinking of a way that he could explain this to the medics.
Going to the hangar and hopping in a Z-95 Headhunter starfighter, Chief seized the controls before blasting off into the densely packed Coruscant skies. Making his way past the enormous naval blockade, Chief landed on a Acclamator that was heading in the direction of his mission area. Quickly making his way up to the bridge, 117 cleared it with the clone commander on duty. The Acclamator would make a brief detour to Eriadu before continuing on to Bespin where they were scheduled to make a fuel pickup.
Informing Chief that he'll instruct maintenance to top off his starfighter before he left and add some extra supplies, the clone commander gave a light smile as he watched the giant armoured behemoth exit his command center. Reaching a private officer quarters, Chief took out a data pad that Fordo had given him for the mission. So far he only knew that it was on the molten planet of Mustafar and that Republic forces were nowhere near the region to assist the special forces team that was present.
Reading further into the casefile, Chief eventually found the name of the strike group. An elite group of altered clones with desirable mutations that were listed as the 2nd most effective special forces unit in the entire GAR. The first obviously being the Master Chief himself. Reading over the name again, Chief almost broke his stern silence, Clone Force 99; "The Bad Batch".