Disclaimer: I own nothing and make no money off this story. All rights go to Lucasfilms. Hope you enjoy my twist on this story.
Cykron, Underground Bar
Rahm Kota was led through the streets into a seedy looking bar. It seemed like every other dive bar until the pirates went up to a wall. The wall opened a panel that revealed a keypad and eye scanner. After the authorization was complete the room rumbled. The entire bar began to sink into the ground. They descended 20 stories before suddenly stopping. They had appeared in a large underground stronghold. They were gun emplacements and launch bays for ships all around. In the center of the room sat a large throne. Kota saw that the pirate king was back to his former glory. He slowly walked forward and bowed his head. Hondo Ohnaka smiled and asked, "What is a Jedi doing here? I thought that your Chancellor had wiped you all out." Kota grimaced at that but kept his tone respectful. He looked up and said, "You had tried to ransom Count Dooku to the Republic near the beginning of the clone wars. He was a Sith which is the opposite to us Jedi. It turns out the leader of the Sith was our Chancellor. He fooled us all and managed to turn most of our clone army against us. With his political position and our army behind him, he was able to facilitate control of the galaxy." Hondo pondered this and asked, "Why did you come here? What is it you want from me?" Kota bowed his head and said, "We are trying to rally allies. We want to fight back against the tyranny of the Empire and restore peace to the galaxy. Will you help us?" Hondo laughed and said, "You Jedi really crack me up. I see no reason to put myself on that psychopath's radar. I have rebuilt my empire and I want to stay in one piece." Kota sighs and says, "As you wish, I will be leaving now." Hondo's men cock their guns but the pirate king tells them to stand down. He looks at them and says, "I may not help them but I will not hinder them. While I won't be a part of this war, I can't wait to see how it turns out."
Cykron
Kota left the pirate stronghold and returned to his ship. He entered the planet's atmosphere and typed in the coordinates for the N.G.R. The council wasn't going to like the news.
N.G.R. Secret Base, Storage Warehouse
The moment that Jaybo was brought back, he began to work. Various scrapper teams had brought him endless supplies to work with. With all the material in place he set up a command station. He started by building some simple B-1 droids and reprogrammed them to find more of their brothers. Once he had 50 built he switched to building an assembly line. He could program the B-1s and have them start assembling their brothers. He got that started in about a week. He had all the B-2 droids outfitted with jetpacks. Once he was done with this army the B-2s would be much more effective in aerial combat. His excitement grew when he saw Droidikas and Commando droids. He tinkered with the droideka shields, he wanted to see if he could increase the power output. After a few hours he grew frustrated and moved his attention to the commando droids. He removed a chip from one's head and began to study the code. They were programmed with incredible fighting styles and agility. Their vocabulators and ability to deceive people were incredible. He was able to copy the commando's abilities and adjust them. This adjusted code was applied to the standard B-1 droids. This new upgrade made them formidable opponents.
He copied the technology that the vocal emulator used and applied it to the B-1s, all they would have to do is listen on comms for awhile and the B-1's could sound like anyone. These new upgrades allowed commando droids to lead armies of B-1s and achieve victory through superior ability and strategy. Jaybo then had an idea for the droideka units. He called Obi-Wan down to the warehouse and waited. After a few minutes Obi-Wan arrived and said, "You've been busy Jaybo." He looked around and saw the production rate. It was able to increase exponentially with more droids putting their brothers together. Jaybo smiled, he was proud of his work. He looked at Obi-Wan and said, "Of course, I never do a job half-assed. The reason I called you here is your battle experience. Who was the best enemy Admiral you ever faced? Who was able to consistently beat your armies back?"
Obi-Wan thought about that and was tempted to say Grievous but that's not right. Grievous was a good general but he focused on numbers and blatant tenacity. He looked at Jaybo and said, "Probably, Admiral Trench. His skill as an Admiral was unrivaled and he beat us more times than I like to remember." Jaybo thought about that and asked, "Did his ships have any special modifications? Did he have any tech that was difficult to get past?" Obi-Wan replied with, "Yeah, Thermal Shields. They blocked our powerful turbo lasers and any solid projectile. Anakin was only able to get past him when he made Trench lower the shields." Jaybo smirked and said, "That's it. These droideka units are great for the front lines but their shields will buckle and fail under a barrage of Imperial fire. I can start outfitting the droideka units with thermal shields and the Imperial front lines will break. Thanks for the help." Jaybo turned back to his computer and started typing a vast set of commands into the screen. Obi-Wan smiled at the ambitious mind and left to go oversee new recruit training.
N.G.R. Secret Base, War Room
Plo-Koon, Mace Windu, and Yoda all stood around the Holo-terminal. Their growing army needed weaponry and ammo, if they were to keep pace with the Empire. Captain Rex and Embo walked in and waited for instructions. Mace turned to them and said, "We have a new mission. This is another retrieval mission but you need to be prepared for heavy resistance. We sent out a team of clones for recon and we just heard back. The Empire has a heavy presence on that planet and you need to be prepared for anything. Your normal tactics won't work. The Empire has started using conscripted soldiers and they have started to use highly encrypted com's. So far we haven't been able to break it." Rex looked at the Jedi Master and asked, "Where are we going sir?" Windu looked at the veteran clone with a serious look and said, "Rothana, you are going to steal ammunition and weapons. To ensure this operation goes smoothly we are dispatching Master Plo-Koon and Jedi Knight Ahsoka Tano." Plo nodded and left to get Ahsoka ready. She had grown stronger since she left Coruscant. He knew she was ready to join him and fight to free this galaxy.
Rex and Embo left as well. Rex needed to get his men ready and plan their arrival. Embo went to meditate and check his weapons. Rex was lost in thought on his way to the barracks. This wasn't going to be like their hit and run missions. There was a high chance that they would have to kill large numbers of their brothers on this mission. He still thought about the firefight of the last mission and memories started to flash through his mind. This reminded him of the tragedy of Umbara and the carnage of Krell. He needed to talk to Cody and Jesse