The Normandy crew with the assistance of Commander Cody, Captain Rex, and a small battalion of clone troopers have just arrived on Quesh to stop a pirate incursion led by a branch of the Black Suns criminal organization. The pirates quickly try to form a blockade while trying to destroy the tip of the spear, the Normandy, but the cruiser keeps flying forward towards Quesh. Dr. Brynn Cole and recent Grissom Academy graduate, Dr. David Archer and a team of other geniuses managed to reverse engineer Reaper tech without the risk of indoctrination and integrated the tech into all currently active Milky Way military ships. The Normandy, a stealth cruiser now had the shields, armor, and firepower akin to a dreadnought. As the Normandy gracefully entered Quesh's atmosphere, it had already destroyed one of the pirates blockading ships and crippled another.

On the ground, Commander Cody layed down suppressing fire on a large group of pirates while Garrus sniped the leaders from a distance and managed to kill three pirates with one shot. Meanwhile, Commander Shepard and Rex went into a jungle area where the Quesh branch of the Black Sun's main base was located. There they found the Black Sun leader and the Banking Clan senator Nix Card being guarded by a squad of repurposed HK assassin droids. Rex suggested they fall back and wait for reinforcements, John Shepard instead biotic charged the group and then proceeded to gun down the HK droids and black Sun leader with his Avenger assault rifle which had been modded with disruptor ammo. Rex and Shepard then took Nix Card prisoner and are now on route to Coruscant to be put on trial.

John Shepard was alone in his personal cabin until Tali appeared and nervously, yet proudly informed him that she was pregnant with his child. Happy, yet utterly shocked John asked how this was possible. Tali then exclaimed that while they were on Odessen, she found data from a late Dr. Eckard Lokin, a scientist that lived 3000+ years ago in the Rayath Galaxy. The data cluster was about gene-splicing two different species, Tali with the help of STG spliced her DNA with human DNA and then one night with John, it happened.

John then lovingly embraced Tali, but was then interrupted by a call from Admiral Hackett. John told Hackett that he found over a dozen ancient lightsabers that all still functioned and that he was taking them back to the Milky Way to be studied. Hackett then told John that he was being promoted to the rank of Captain and that he would've promoted him sooner, but he was too busy keeping the peace and rebuilding both the military and the government. Captain John Shepard then humbly thanks Hackett as the Normandy jumps into hyperspace.

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On the outskirts of Coruscant, Darth Sidious was waiting for Dooku to arrive, fully expecting him to try and kill him, but something was different, Sidious could sense that his apprentice had grown significantly more powerful in the force. As soon as Dooku entered the room Sidious fired off full powered force lighting to end the fight before it even began; however, Dooku swatted away the lighting like an insect and then proceeded to duel Sidious with their lightsabers. An hour into the duel and Sidious was losing ground, his mind was filled with

unbridled fury and confusion as to why he hasn't already crushed his former apprentice. Sidious quickly broke away from the duel and once again shot force lighting at Dooku, but not only did Dooku effortlessly redirect the lighting back at Sidious, Dooku fired his own force lighting and within minutes Sidious was incinerated and reduced to nothing but a smoldering pile of bone and ash.

2 weeks later, Dooku had the seperatist council quietly assassinated and then had the CIS held a senate meeting where he then began to use a more powerful version of the mind trick, force submission to make all members of the senate fiercly loyal to him and had them restructure their democratic government into an empire with Dooku as emperor. Dooku then christened it, the 'New Sith Empire'.

Shortly after, a group of scientists from the Milky Way went into the Rayath Galaxy seeking refuge, they claimed to be from a now defunct organization, Cerberus. They told Dooku of the projects they worked on, some were developing more advanced AIs and weaponry while others said that they focused on cloning and actually made a successful clone of John Shepard. Upon hearing all of the new information, Dooku smiles and exclaims that he and the empire will provide them sanctuary on the condition that they continue their work for the empire.

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The Galactic Civil War had reached Kamino, the clone troops were barely holding on to the planet even with their weapons being upgraded with mass effect technology and with the jedi numbering in the hundreds. Under Dooku's orders, Grievous was leading the attack with thousands of battle droids, but Grievous and the droids were different. They were faster, stronger, more durable, and better skilled than usual and what's more strange is that all the battle droids, even the basic ones are displaying increased intelligence and better leadership skills. Inch by inch the droid army advanced, taking out clones left-and-right. As more Jedi entered into the fray, the Republic armies had managed to make the droids hunker down and began to push them back. This battle of attrition had seemed to finally tip in the Republic's favor.

As the Grievous and the droid army fell back, they stopped, hunkered down, and fought even harder. Grievous quickly jumped into a hastily made bunker and pulled out a communicator and ordered the next phase of the attack to begin. A dozen imperial ships appeared in Kamino's sky and landed. What came out of the ships was an army of not more droids, but one thousand humanoid troops dressed in black and appeared to be carrying lightsabers, RED lightsabers.

Dooku had the ex-Cerberus scientist create a clone army using a hybrid of both mass effect and rakatan technology and programmed the clones to be fiercely loyal to both Dooku and the Sith Empire. The clones themselves were cloned from the combined DNA of Captain John Shepard and Emperor Dooku himself. Dooku used memory flashes to educate the clones on how to wield a lightsaber and how to use the force enough so that they can fight both the jedi and clones troopers effectively, but not enough in the unlikely case that they gain free will and attempt to rebel. Dooku called his new clone army the Inquisitors.

The inquisitors and wardroids then began to mow down the jedi and clone troopers in droves and began to enter into the heart of the cloning facilities. They then began to massacre the kaminoan scientists and destroy all their data on cloning, after this the imperial army entered their ships and went outside of Kamino's orbit where they're met with even more imperial ships. This imperial fleet then began to fire on the planet itself with everything they had, the oceans evaporated and the land itself was glassed over. This was the day the Sith Empire cut off the arms of the Republic.