As The ship flew away Master Yoda turned to Windu "if Dooku escapes rally more systems to his cause he will" he warned as the ship then was fired upon. On Jason, Obi-wan, and Anakin's ship they to held on tightly as the ship dodged the blaster fire. They were heading towards a Techno Union Ship and Anakin turned to the pilot "aim right above the fuel cells!" he instructed as the ship fired missiles and destroyed the target. "Good call Anakin!" Jason praised patting him on the shoulder as the remaining Jedi and clones fought on the ground.
In the command Spire Dooku and Viceroy watched the battle unfold. "The Jedi have a massive army" Viceroy commented. "That doesn't seem possible, how can the Jedi assemble an army so quickly" Dooku said shockingly. "We must send all available droids into battle!" Viceroy suggested. Dooku shook his head "there are too many" he told him. The Geonosian leader spoke up "they have disabled our communications" he said frustrated.
Yoda and Windu's ship continued to fly as they watched a ship next to them blow up. "Pilot! land in that assembly area" Windu ordered as they landed. A clone commander walked up to Windu "sir I have special commando units awaiting your orders sir" he said which Windu nodded as they walked away. "To the forward command center take me" Yoda ordered as the ship took off. Meanwhile on Jason's ship Obi-wan noticed the Federation ship flying up "attack those Federation starships quickly!" he ordered as the ship continued to fire until the starship tumbled down destroying a lot of droids in the process.
In the Spire Viceroy looked at the battle and sighed "this is not looking good at all" he commented. "We must get the starships back into space" Rune told him as they walked to the nearest ship and flew away. "we have to order a retreat" the Geonosian told Dooku. "My master would never allow the Jedi to get away with this treachery" Dooku denied. "I'm sending my warriors to hide in the catacombs" the Geonosian told him. "The Jedi must not find out our design for the ultimate weapon" he continued as he transferred the data on the console in front of him to a personal datadisk "if they find out what we are planning we are doomed" he spat as he handed Dooku the datadisk. "I'll take the design with me to Coruscant, it will be much safer there with my master" Dooku said before deactivating the device. As he mounted his speeder bike and sped off with two ships on his sides Viceroy and Rune entered their shuttle and took off.
The battle raged on as losses on both sides grew with the clones advancing. Aboard Obi-wan and Anakin's ship Obi-wan took notice of Dooku on his speeder bike "look over there!" he said pointing in Dooku's direction. "It's Dooku! shoot 'em down!" Anakin ordered the pilot. "We're out of rockets sir" the pilot told him. Anakin sighed at that "follow him" he ordered as Padme got their attention. "We're gonna need some help" she exclaimed. Obi-wan shook his head "there isn't time, Anakin, Jason and I can handle this" Obi-wan told her. Meanwhile Dooku took notice and ordered the two ships to fly away. When they did they went behind the clone ship and started firing causing the ship to swerve and dodge. When they hit the ship it toppled causing Padme, Melaena and Jason to fall off with Anakin calling out to them. "Put the ship down!" Anakin shouted. "Anakin don't let your personal feelings get in the way" Obi-wan warned before turning to the pilot "follow that speeder!" he said as the ship continued following Dooku. "Lower the ship!" Anakin persisted. "I can't take Dooku alone, I need you if we catch him we can end this war right now! We have a job to do!" Obi-wan tried to get through his apprentice. "I don't care put the ship down!" Anakin denied ignorantly. "You will be expelled from the Jedi Order!" Obi-wan warned frustrated. "I can't leave them!" Anakin told him. "Come to your senses, what would you think they'd do if they were in your position?" Obi-wan asked him. That caught Anakin off guard causing him to take a deep breath and think "they would do their duty" he muttered causing Obi-wan to nod.
Meanwhile one of the clone commanders who was overseeing the battle with Master Yoda turned to the elder Jedi. "The droid army is in full retreat" the commander told him. "Well done Commander bring me a ship" Yoda ordered before the commander issued said order.
With Anakin and Obi-wan they continued forward as Dooku sped inside one of the buildings. When they reached the platform the two Jedi jumped down activating their lightsabers in the process before the ship was destroyed. They ran inside and were greeted by Dooku who stood but a few feet ahead. "You're gonna pay for all the Jedi you killed today Dooku" Anakin warned. "We'll take him together you go slowly on the left-" Obi-wan was quickly cut off by an angry Anakin "no I'm taking him now!" he said sprinting towards Dooku. "No Anakin No! No!" Obi-wan warned as Dooku hit Anakin with Force Lightning causing the young Jedi to tumble down in pain. Obi-wan pointed his lightsaber at Dooku defiantly. "As you can see my Jedi powers are far beyond yours, now back down" Dooku warned sending another wave of lightning which Obi-wan blocked with his lightsaber. "I don't think so" Obi-wan told him. In response Dooku activated his own blade and Obi-wan lunged forward and the two exchanged a few counters before Obi-wan backed away as Dooku dodged a leg cutting blow. "Master Kenobi you disappoint me, Yoda owes you in such high esteem" Dooku mocked before attacking which Obi-wan blocked. Dooku smirked "surely you can do better" he continued to mock as he effortlessly blocked Obi-wan's attacks. While they fought Anakin finally regained consciousness and groaned in pain.
Meanwhile Jason, Padme, and Melaena also regained consciousness as a clone trooper knelt down at them. "Are you alright?" he asked them getting confirming nods. "We'll need to head to the forward command center" he informed them. Padme shook her head "no, no gather what troops you can we've got to get to that hangar, get a transport" Padme ordered. "You guys go on ahead I'll get there my way" Jason told them which Padme nodded before they ran away. Jason then closed his eyes and focused the Force and flew up speeding towards the battle ahead with a look of determination on his face.
In the lightsaber battle Obi-wan continued trying to gain the upper hand but to no avail. As Dooku blocked another strike Obi-wan pushed to the side as Dooku smiled in sadistic glee before slicing at Obi-wan's arm causing him to gasp in pain. To add to the injury Dooku stabbed Obi-wan's leg causing him to fall down. Anakin noticed Dooku about to make the final blow and lunged forward blocking the attack. "Brave of you boy, I'd have thought you learned your lesson" Dooku mocked as Obi-wan used the Force to grab his lightsaber. Time to show what Jason has taught you Obi-wan thought. "I am a slow learner" Anakin said as Obi-wan called out to him throwing his lightsaber at him which the young Jedi caught and engaged Dooku. Dooku managed to slice Anakin's green lightsaber leaving him with only one left. He then cut a power line causing the lights to flicker off. Anakin then resumed his attack on Dooku which the older man held his own. When it seemed Anakin could win Dooku swung around and sliced Anakin's right arm clean off and Force pushed him right next to Obi-wan. He then deactivated his lightsaber before hearing footsteps behind him. He turned around to see Jason clad in his black robes "Jason Pandora" Dooku greeted. "Count Dooku" Jason sneered as he glared. "You and many others have interfered with our affairs for the last time" Dooku said as he used the Force to send a piece of machinery at Jason who stopped it and pushed it away. Dooku tried again and Jason once again stopped it and swung it away from him. Growing frustrated Dooku used the Force and grabbed the ceiling causing the debris to fall down towards Jason. Jason still blocked it much to Dooku's dismay. "You have become powerful Dooku, the dark side I sense in you" Jason commented as Dooku regained his composure. "I have become more powerful than any Jedi, you will not be the last" he said as he sent a wave of lightning at the Jedi. Jason used the Force and blocked the attack and sent it right back at the fallen master who blocked as well before sending another wave. Jason then crushed the attack into nothing as Dooku went for his lightsaber. "You still have much to learn" Jason told him. Obi-wan was right, he has become more powerful than I had anticipated Dooku thought. "It is obvious that our contest cannot be decided by our knowledge of the Force, but by our skills with a lightsaber" Dooku said s he swung his lightsaber threateningly. "So be it" Jason muttered before activating his two lightsabers. Uttering a war cry Jason lunged at Dooku with a speed even Dooku hadn't anticipated and engaged the fallen master. As they fought Dooku started to struggle to keep up with the young knight before Jason blocked causing the two to come face to face. "You fought well, just like a padawan" Jason mocked causing Dooku to grit his teeth. "This is just the beginning" Dooku warned as he used the Force on one of the pillars and caused it to tumble down, about to crush Obi-wan and Anakin. Noticing this Jason quickly deactivated his lightsabers and used the Force to try and stop the pillar from crushing his friends allowing Dooku to escape in the process. As Dooku's ship flew away Jason used everything he had at stopping it. When he was forced to one knee and his eyes clenched he struggled desperately to hold the pillar. Obi-wan looked over at his friend sadly before noticing when Jason opened his eyes they were completely white and the pillar finally stopped just inches away from Obi-wan's face. The pillar was then moved over and finally dropped down along with an exhausted Jason who passed out. The clones along with Padme, Melaena, and Master Yoda entered the room only to see a limping Obi-wan, an injured Anakin and an unconscious Jason. "Jason!" Padme exclaimed running over to her beloved as Melaena hugged Anakin tightly. Master Yoda hobbled over to Jason and sighed in relief "alive, he is" he told Padme before the clones picked him up and got everyone medical attention.
As Dooku's ship reached Coruscant he sighed heavily. His battle with Jason had weakened him greatly, he had never faced a foe so young but so powerful. The ship reached a dark part of Coruscantand the hangar door in front of it opened before it landed. Darth Sidious stood waiting as Dooku walked down the ramp. "The Force is with us Master Sidious" Dooku said to the Dark Lord. "Welcome home Lord Tyranus" Sidious greeted as the two walked side by side "you have done well" Sidious praised. "I have good news for you my lord, war has begun" Dooku informed him. Sidious smiled evily "Excellent, everything is going as planned" he said. His cackling echoing the walls of the building.
Meanwhile after getting their wounds treated Obi-wan and Jason stood with Windu and Yoda in the Jedi Temple. "You think Dooku was telling the truth about Sidious controlling the Senate? it doesn't feel right" Obi-wan questioned as he and Jason stood in front of the window. "Joined the dark side Dooku has, lies and deceit create mistrust are his ways now" Yoda told them. "Nevertheless I think we should keep a close eye on the Senate" Windu said. "I think we should focus on the Chancellor the most" Jason told them causing them to look at him. "Why the Chancellor specifically?" Windu asked. "It's just ever since my battle against Darth Maul I have been feeling very uneasy around the Chancellor" Jason admitted. "I agree" Yoda assured him as the other two nodded. Windu then turned towards Obi-wan "where's young Skywalker?" he asked. "He's on his way to Naboo, escorting Senator Amidala and Representative Pandora" Obi-wan told him. Jason looked a bit uneasy, he knew the real reason why Anakin went to Naboo but he promised to keep it a secret "How is your relation with Senator Amidala Jason?" Windu asked. That caused a smile across Jason's face "we are engaged to marry in a few weeks" Jason told them which Yoda smiled. "Congratulations on your engagement I offer you" he told Jason. "Thank you Master Yoda" Jason thanked causing another grin on the old Jedi's face. "Another offer I have for you" he said causing the young Jedi Knight to give a confused look "because of your battle against Dooku, a place on the council you have" Yoda said causing Jason's eyes to widen. "A Master? I- thank you Master" Jason said bowing deeply. "I do have to say without the clones the battle would not of been a victory" Obi-wan cut in. "Victory? Victory you say? Master Obi-wan not victory, the shroud of the dark side has fallen, only begun the clone war has" Yoda warned causing the three other Jedi to stare out the window pondering what future awaits them.
Chancellor Palpatine and the other Senators watched as the clones boarded their massive starships knowing that this was only the beginning.
Later on Naboo Anakin and Melaena stood across from each other in wedding robes along with Jason and Padme watching. When they finished their vows Melaena grasped Anakin's now mechanical hand and the two kissed passionately with Jason and Padme cheering. When they parted they stared lovingly in each others eyes. While applauding Jason was suddenly pulled over by a grinning Padme who smashed her lips on his and the two stood embracing one another.