"NOOO!" Anakin screamed as he woke up.

"Ani, what's wrong?" Padme asked as she was woken up by his scream.

"I...I had a vision about the Chancellor." Anakin shaked his head.

"What vision?" Padme asked worriedly.

"That Palpatine is the Sith Lord that we've been looking for." Anakin replied as Padme gasped in shock "I need to inform Obi Wan about this."

"Whatever you do, please becareful I don't want to lose you." Padme said her eyes filled with tears.

"I know my angel, I'll stay alive for your sake." Anakin assured her and left, contacting Obi Wan on the way "Master, I must meet you now, it's important bring Cody and Rex with you I have a feeling that we need them."

"Of course Anakin, I'll be there shortly." Obi Wan's voice sounded as if he was in a rush.

Anakin waited impatiently for Obi Wan to arrive and after two hours of standing, a gunship arrived and landed on the landing pad. Anakin rushed to greet Obi Wan who managed to convince Cody to give up the search for General Grevious and Rex who was having a secret meeting with Ahsoka. "Master, Rex, Cody, I'm glad to see you guys, come in, we have much to discuss." Anakin said beckoning them to enter.

Anakin told them about his vision "Hold a moment for there, you're telling me that Chancellor Palpatine is the sith lord!" Rex shouted causing Cody to fall off his chair.

"How many times must General Skywalker repeat himself, yes that old man is a sith lord!" Cody yelled back as he stood up.

"Old man?" Obi Wan asked hiding his smile.

"Well, I never liked that old bastard anyway so what's the plan I'm in." Cody replied with a grin and he turned to look at Rex "How about you?"

"If it means a pay raise, I'm in." Rex said.

"Okay, the plan is this we need to convince most of the troops that Chancellor Palpatine is evil so they will not carry out his order if he gives it. Next, we need to ensure the safety of the Jedi Temple are you up to it Rex?" Anakin asked as everyone turned their gaze to Rex.

"I sure am, what's more I won't let anyone harm Ahsoka!" Rex agreed.

"Cody, I need some of your men to protect the younglings that will surely panic during the attack." Anakin said.

"I'll do what I can, you have my word." Cody replied.

"Then the Resistance begins here, tonight, we must not let anyone knows about this even Master Yoda." Anakin said as Cody, Rex and Obi Wan nodded.

A few days later, Jedi Master Mace Windu and three other masters attempted to arrest the Chancellor but failed. Out of all the Jedi who went only Mace Windu survived but was injured. "Commander, the time has come Execute Order 66." Palpatine said in a harsh tone.

"Yes my lord." the commander replied before disconnecting and turning to his men "I'm not going to listen to him, we must ensure that General Mundi does not die."

Plo Koon was flying his starfighter when an explosion sent a clone fighter crashing down, he turned around to see who is attacking what he saw made him stare in shock. Yoda was observing the troops when he sensed something wrong, he turned around to see a dead trooper and Gree standing over the body. Ki-Adi-Mundi ordered his men forward, when he heard blaster sounds behind followed by countless of clones screaming in pain, he froze and turned around slowly. Aayla Secura was looking around for droids when she heard blaster sounds and turned around to her surprise, she saw Commander Bly and a few of his men standing over four dead clones. All across the Galaxy, clones were fighting among themselves, their Jedi Commanders could only stop and stare as they fought each side yelling 'For the Republic!' and 'Down with the Chancellor!'

Back at Coruscant, things were looking pretty well for Anakin. "Hurry, we must fool Palpatine, Rex over here!" Anakin's voice echoed down the Jedi Temple causing everyone to wake up. Jedi Master Shaak Ti woke up to see members of the 501st legion and the 212th battalion running in all directions , some were arranging fake bodies on the ground others were throwing wood to a bonfire causing a huge column of smoke to rise, her eyes spotted Clone Commander Cody and Obi Wan smashing the Jedi Temple windows. She walked towards Obi Wan and Cody "Master Kenobi, what is going on here?" she demanded.

"Not much Master Ti, we are just making sure that the sith lord is fooled." Obi Wan replied politely before turning to Cody "Gather the younglings and bring them on board the cruisers and set off immediately, it won't be long before the Chancellor's elite soldiers arrive!"

"Yes General." Cody replied and ran off yelling "Boil, you take the west side!"

"Rex, what's going on?" Ahsoka asked awaking from her sleep.

"Nothing, Ahsoka we are just preparing a welcome party for the Chancellor's men." Rex answered as he threw more logs into the bonfire. Ahsoka gave up and went to look for Anakin when she noticed Fives carrying lots of archive records out of the Archives. "Hey Fives, what are you doing?" she yelled.

"Ah, there you are Ahsoka, would you mind giving Slug a hand he's very slow." Fives responded with a smile before taking off in a rush.

"Master Nu, what is really happening?" a padawan asked.

"Master Skywalker says that we must evacuate, Olee you can help me by carrying all these records to that gunship." Master Nu replied.

Within minutes, the entire Jedi Temple looks as if it had been attacked. Anakin and Obi Wan looked on smiling at their accomplishment. Cody and Rex had a hard time rounding up the younglings and junior padawans but found it easier when Ahsoka came to help. Fives with the help of several knights and senior padawans managed to clear the entire Archives of records, leaving it empty. Boil took a detachment and cleared the training rooms, taking everything from training helmets to lightsaber components. Shaak Ti also decided to help and packed every important thing a Jedi needs to survive.

"We've done it Anakin, everyone is on board the Repulse." Obi Wan smiled.

"Admiral, jump to hyberspace, we must get out of here." Anakin ordered with a grin.

"As you command general." Admiral Yuralen replied with a smile and ordered the jump.

"Cody, Rex, contact the rest of the commanders, tell them to meet us on Yavin." Anakin said with joy in his heart.

"Yes general." both Cody and Rex replied and rushed off to contact the rest.

Mace Windu woke up to find himself in a medical ward, he hopped off his bed and realised he was in a star cruiser. "Master Windu, you've awaken I was fearing the worst." Shaak Ti said with relief as Mace Windu stared with shock at the amount of younglings and padawans that were resting.

"How...I heard Palpatine gave the order to kill all Jedi." Mace managed to say.

"You have to thank Skywalker for this." Shaak Ti smiled as Mace wondered.

"Where is he?" Mace finally said.

"In the gym with Master Drallig and Master Kenobi." Shaak Ti said as she helped Mace to his feet.

"That's right, feel the Force in you." Anakin said calmly as the group of padawans deflected the laser bolts that Cody fired.

"Anakin, I'll take over it's Mace." Obi Wan said as he pointed to Shaak Ti.

"Master Windu!" Anakin exclaimed with joy as he hugged the shocked Mace "I knew you'll come back to us!"

"Anakin...thank you for saving me." Mace said with gratidute in his voice.

"No problem Master Windu, we will be arriving on Yavin in a few hours, I suggest you take a rest it won't be long until the rest of the council joined us." Anakin said with a smile and turned around.

A few hours later, several other star cruisers also arrived on Yavin. "This is Admiral Yuralen, what's the password?" Yuralen demanded before he'll allow them to land.

"Chosen One." Commander Wolffe replied.

"Permission granted, welcome back Wolffe." Yuralen said with a small smile.

Yoda, Plo Koon, Ki-Adi Mundi and the rest of the Jedi that were sent out to fight walked out of the landed star cruiser with a shock look on their face. The entire land has been transformed into a full time operational clone base, there were 501st legion patrolling and 212th battalion troopers training with the senior padawans. Younglings were also training under the watchful eyes of Master Cin Drallig and Obi Wan Kenobi. Anakin and Mace went to greet them "I'm glad to see all of you masters." Anakin said as Mace smiled warmly.

"General, we've managed to save what Jedi we could though we lost some of our own." Commander Bacara said with a salute causing the Jedi to stare in shock.

"I'm sorry for the loss of your men, what of the traitors?" Anakin said as if he was their leader.

"Dead to the last man." Commander Gree said as he removed his helmet "You can say, I saved the Grand Master life!"

"Only one, listen here Gree, I saved two padawans, four knights and three Jedi Masters beat that!" Commander Wolffe argued.

"Hey, I saved twenty younglings, fourty junior padawans and five masters!" Rex shouted as Cody shaked his head.

"Look guys, we better start forming the Resistance army right now." Commander Bacara suggested as the other commanders fell silent and nodded.

"Thank you Bacara, I can't wait to hear how you saved Master Mundi." Anakin said with a smirk "Now, come along, much to discuss we have."

The commanders looked at each other and followed Anakin to the command center leaving Mace to deal with the confused Jedi. "Master Yoda, Skywalker did all this, can you believe it." Mace said with a smile.

"Believe him I do, saved the Jedi Order he did, make him a master we should, all in favor." Yoda asked as the response nearly knocked him down.

"AYE!" the twelve council members shouted in unision.

For the next few years, the Jedi Order would continue on in secret far from the eyes of Palpatine. Even though Palpatine became the Emperor, he only have a few clones on his side, he was shocked when he discovered that Admiral Yuralen and a few other improtant admirals have disappered.

Anakin Skywalker was given the rank of Jedi Master and was given a seat at the Jedi Council, he leads the new resistance army and after much of Obi Wan's annoying visits he decided to take a padawan learner. Obi Wan on the other hand began to teach younglings about the ways of the Force but still had close contact with Cody and the 212th battalion.

Mace Windu had thought long and hard about the attachment code and decided, he brought up his suggestion to the council that the code be taken away and Jedi are allowed to fall in love. Much to Anakin's amusement when Obi Wan immediately declared that he is going to marry Duchess Satine. Mace Windu finally declared his love for Aayla and the two had a brief wedding.

With the attachment code gone, Ahsoka married Rex and both of them had twins. Ahsoka decided to name the boy Rexan and the girl Soka. Rexan was force sensitve and wanted to become a Jedi like his mom while Soka wanted to be a captain of the resistance like her father.

The 501st legion continued protecting the planet from any imperial presence while Yuralen travelled far and wide bringing back more younglings with each trip he made. The 212th battalion worked closely with the Jedi Knights in ensuring the safety of the new Jedi Temple. The remaing troopers quickly formed into different types of squadrons the most famous led by Commander Bly he called it the Chosen Squadron causing Anakin to chase him around demanding an apology.

Commander Gree decided to step down from being a commander and become a caretaker for the Jedi younglings, he would soon regret his decision when Yoda brought home a hundred of his kind.

Bacara took his free time to help Gree looking after the hundred baby Yoda which Yoda had adopted as his sons and daughters. Wolffe decided to help Obi Wan train the younglings much to Cody's amusement. Anakin had also brought Padme and his two children over for protection, leaving Bail Organa to keep spying on the Empire.