Jedi Temple - Coruscant
Even though Barriss Offee was deemed the traitor that bombed the Temple, there was still no sign of Ahsoka. Leaving Anakin devastated, feeling that he had really lost her this time. As a result, the Council paired him with Master Kenobi again for the time being whilst their two units did a combined offensive in the Outer Rim.
But before the fleet departed, the Council called in Skywalker, Master Chief and Captain Rex to one of their briefing rooms. Explaining that the renegade Sith Lord Darth Maul has seized the planet of Mandalore and that Bo Katan of the Night Owls has requested Republic assistance in taking back the planet. The Council had reviewed the intel provided by Lady Bo Katan and deemed Maul as a credible threat.
However, Skywalker and his men were still needed to help the offensive in the Outer Rim, meaning that they could only send one ship to the battle. Seeing where this was going, Chief merely sat back and listened as Windu ordered the spartan and clone to command the operation on Mandalore alongside Bo Katan.
Expecting outrage from Skywalker, Chief heard none. Anakin informed the two that he trusted them with his life and the lives of every man they were taking with them. Saluting the two generals in the room, Chief and Rex left to go board the Intrepid.
Time skip
Nevaro
In recent months the 501st had grown exponentially in numbers given their string of victories, earning them access to more clones, tanks, starfighters, ship etc. Now the 501st was made up primarily of three Venator class cruisers which included the Independence, Intrepid and Resolute, the last being the flagship. However, the fleet often got more ships to tag along depending on what the operation was and what the 501st needed.
But for the Mandalore operation, only one Venator was needed and the Intrepid was the ship for the job. Outfitted with improved point-defense cannons and missile launchers, the Intrepid was more suited to fight against hordes of starfighters compared to fighting large battleships. The reason for this being that it carried a reduced starfighter compliments of only 6 ARC-170's, 20 Y-wings, and 16 V-wings.
But the lack of starfighters was definitely made up for in cargo space for ground assault vehicles including LAAT gunships, AT-TE walkers, AT-RT scout walkers, BARC speeders and AV-7 cannons. Meaning that this ship was perfectly suited to take on the full force of what Mandalore had to offer.
As some Night Owl transports landed in the hangar bay, Captain Rex walked out to greet the arrivals of the Mandalorian part of this invasion. But as an added precaution, the Bad Batch was also tagging along for this assignment. Turns out, the criminal empire that they were tracking the last couple of weeks led right to Maul and his Mandalorians.
So while Crosshair, Tech and Wrecker were getting ready onboard the Marauder, Hunter was walking with Chief up to the command centre so that they could go over the plan with Bo Katan. After introductions were made, the group got right into it, the 501st would make a direct assault on the Capitol with support from the Night Owls. After securing a foothold, tanks could be brought down alongside medical aid for any civilians caught in the crossfire.
Captain Rex would secure the streets, the sooner they got control of that, the less civilians would be hurt. The puppet ruler Almec would probably be held up in the prison compound, the most fortified building in the city. Bo Katan alongside Clone Force 99 would take care of that, leaving Maul. "This is why I wanted a Jedi to come." Bo pointed out.
"Don't worry, we have him." Hunter said, pointing his thumb towards Chief. "Ah yes, the spartan. Your kind fought for the Old Republic, destroying entire armies for them. We tell stories about your combat prowess to the children, making you out to be the greatest warriors in history, second only to the Mandalorians of old. Now we'll see if those legends are true, spartan."
Time skip
Mandalore
Just like they planned, the initial invasion went great as far as invasions go. The city had no anti-air defenses like flak cannons, missiles or even just machine guns. The only resistance they encountered were around three dozen warriors with jet packs. But they were easily dispatched by the LAAT gunships and Night Owl warriors.
As the Marauder landed on one of the occupied platforms, Chief got off along with the rest of Clone Force 99. They didn't want Maul to know that there were special forces on the ground, because if they did; Chief and the Bad Batch would become high value targets that would just draw enemies towards them. This would give both Maul and Almec time to escape, which is something the GAR forces could not afford.
Disappearing like a shadow once more, 117 made his way to the palace undetected before stopping right at the front door. He was waiting for someone to make an appearance, out of nowhere, a tap on his shoulder indicated that his backup had arrived.
Turning around to see Ahsoka wearing some orange painted clone shin guards and gauntlets that were modified to fit her. Chief also noticed that she had both of her lightsabers with her, he briefly asked how she got them. "Master Shaak Ti sent me the 2nd one when the latest batch of men came to the Autumn. I've made some adjustments as well."
Nodding his head in affirmation, Chief kicked down the door to the throne room with Ahsoka right behind him. Looking straight ahead towards the throne, the pair saw Maul just sitting there casually, as if he was waiting of them. "Oh its you... I was hoping for Kenobi... why are you here?"
"Stand down Maul, you are under arrest for crimes against the Republic, smuggling of illegal goods and war profiteering." Chief ordered, not willing to take no for an answer. But Maul just laughed, going on a rant about how the Republic was about to fall and how his Master almost had his new apprentice. "I've seen it, a powerful Jedi turned to an even more powerful sith, yes... All this time we have just been pawns to his game."
"Who is this Jedi you speak of?" Ahsoka commanded, Maul was clearly not just testing Chief's patience. With a scheming grin, Maul looked up. His yellow and red eyes staring right at the pair, muttering in a dark voice; "Skywalker."
"That's enough Maul, surrender now or we will take you in by force. We have you outnumbered."
"Oh I don't think so." Maul replied seconds before the glass windows shattered as six Mandalorians in all black armour landed on the throne room floor. Each equipped with a jetpack and a small armoury's worth of weapons. Leading them was Gar Saxon, the top Mandalorian warrior.
"Chief, I'll take out Maul. You deal with them." Ahsoka said as she ignited two ice blue blades that lit up the entire throne room. As Maul copied her movements but with a double bladed crimson saber, the room broke into a massive firefight. Giving Tano as much space as possible, Chief jumped at Saxon and tackled him through one of the broken windows, causing the rest of the super Mandalorians to follow.
While they were falling, Saxon attempted to break free with his jetpack and fly off, but Chief's grip was too tight. The only thing the red Mandalorian accomplished was slowing the fall down at the cost of overheating his jetpack. As the two landed on the ground, Chief quickly blocked a combo of punches and hit back with a massive head butt, sending his opponent stumbling backwards. Dashing at him, Chief swiftly spun him around and punch a hole in the jetpack, disabling it.
As the other Mandalorians arrived and started shooting at the super soldier, Chief spartan kicked Saxon across the courtyard, knocking him out cold against the concrete wall. Turning around, Chief took out his assault rifle and began firing back to the oncoming Mandalorians. Unfortunately, unlike the rest of Maul's forces, these commandos had untainted Beskaar armour, resulting in Chief's rifle having zero effect. Seeing that Chief's armour was also impervious to their blasters, the Mandalorians landed and deployed melee weapons.
Mimicking them, Chief unsheathed his vibro-blade and got into a combat stance. Launching forwards, the first two tried to attack Chief from the front while also wielding blades. Even though they were very proficient, Chief's experience just dwarfed any training they may have previously had. Swiftly slicing one's throat while catching the other one's arm, Chief crushed the second attacker's right arm before headbutting her unconscious.
Not holding back, the remaining four moved in unison and surrounded the spartan. Igniting flamethrowers and firing away at Chief, 117's shields were almost immediately depleted, his physical armour however, remained untouched. Charging at the closest one, Chief sent a spine shattering spin kick to the left before bringing the commando's head down into a knee uppercut.
The final three didn't do much better, with the last one retreating from the fight after Chief body slammed one of his comrades through a concrete wall. But just before Chief make his way back up to help Ahsoka, he received incoming fire from Gar Saxon who clearly wasn't done fighting yet. Running full force at the downed Mandalorian, Chief launched into the air before throwing a punch so powerful that it went through Saxon's helmet; shattering the yellow visor and causing a large pool of blood to instantly form around his corpse.
Time skip
Intrepid
All aspects of the invasion went perfectly, Maul was defeated and arrested by Tano, Almec was also detained and turns out Chief had taken out all of the top lieutenants in the little brawl in the courtyard. But before they departed, the 501st still had to help restore and rebuild the war torn Capitol.
However, the clone engineers and medics better hurry up down on the surface. Apparently Dooku and Grevious had attacked Coruscant with a massive fleet and kidnapped the Chancellor. But thanks to Skywalker and Kenobi, the Chancellor was rescued and Dooku was even eliminated by Anakin. Suddenly, all the pieces clicked together in Chief's head, Palpatine was the Sith Lord all along, he had created the CIS with Dooku as a puppet to give the Republic a reason to build the clone army.
Now there were millions of clones with inhibitor chips in their brains that could be commanded by Palpatine with zero hesitation. The droids also likely had a kill switch, ending the Separatist and giving the Sith undisputed control of the galaxy. And now with Dooku dead, Palpatine was likely already grooming Anakin to become his new apprentice.
But before Chief could say anything, a transmission from Coruscant came through. As Captain Rex went to the hologram table, a disfigured form of Palpatine emerged, sending waves of hate coursing through John's blood. This was the enemy he was created to hunt, to exterminate, and he had been played for a fool this whole time. "Captain Rex, the time has come; execute Order 66."
But to Palpatine's surprise, Rex didn't acknowledge the order, nor did any clone on the bridge. Because on the way to Mandalore, Rex had all the clones scheduled for a medical appointment with the medics. "Master Chief, I order you to eliminate CT-7567 and every clone on that ship."
"No sir."
"Soldier, I am ordering you to destroy those clones!" Palpatine yelled in anger, he couldnot afford to have a loose cruiser on the run during the most pivotal moment in his plan. But Chief just responded coldly with.
"Go fuck yourself sir."