After a few years of this, Admiral Daala, the only woman to achieve the rank of Admiral in Imperial history, tried to unify the warlords during a conference. When the warlords began to fight, Daala gassed them and took over the various fleets and waged war against various Republic planets. She was finally defeated while attacking Yavin IV, the location of Luke's Jedi Academy. Aboard her command ship, the SSD Knight Hammer, a copy of the SSD Executor, that was painted black to add a fear factor because Republic fleet crew would only see the lights of the viewports. After a TIE bomber misfired a concussion missile into the hangar and set off a series of explosions that disabled the engines. Then, the gravity of the gas giant Yavin began to pull the SSD and it was sucked in and destroyed. The remaining ISD's were pushed 50 light years away when the Jedi students combined their force powers and pushed them away.

After the Adm. Daala incident, Grand Admiral Thrawn, a tactical genius and the only non-human to hold the position of Grand Admiral, was thought dead for several years until he staged a comeback assualt against the Republic. Linking up with the Imperial Union of Allied Planets, the only faction still clinging to the original ideas of the Empire, Thrawn found one of the Emperor's storehouses on a outer-rim world. Known as Mount Tantiss, the storehouse was built into the middle of a mountain and contained several of the items he used during his campaign. Among technologies taken were the Spartii cloning cylinders, which allowed several thousand men to be created in a short amount of time to serve as crewers aboard the Imperial Fleet. Also discovered were the Cloaking shield units, which rendered a ship undetectable by all sensors except for a CGT (Crystal Gravity Trap) which senses mass instead of shape or energy outputs. The cloaking device works at a large cost, however, because the crew is inable to see anything outside of the cloaking field, so they are essentialy flying blind. Thrawn pushed the Republic back in years of progress, and almost won until the Battle of Bil Bringi. The Noghri, a species "saved" by the Empire served as Imp. bodyguards. Thrawn's personal guard discovered that the Empire had kept the Noghri's homeworld devastated instead of improving its enviromental state. Named Ruhka, the Noghri killed Thrawn with his knife (Noghri are excellent knife-fighters) and assasinated Thrawn. After Thrawn's death, the Imperials retreated back and the Republic regained its lost terriory. Thrawn supposively "returned" ten years later, but it was merely a con artist and a clone of one of the Emperor's best royal guardsman setting up an act. When the ploy was discovered, Admiral Pelleaon forged the Treaty of Bastion and established a standing peace between the Empire and the New Republic, which was monitiored by the third party faction Smuggler's Union, headed by Talon Karrde. Under the treaty, Imperial-controlled planets could switch over to Republic control and vise-versa, and open warfare between the Empire and Republic could only be justified if the Treaty was breached, and was justified by the Smuggler's Union.

The next threat to the Republic came from an alien species that had been controlled by the Empire for years. The aliens, called the Yevethans, took control of an entire Imperial battlegroup called the Black Sword Command shortly after the Battle of Endor. The Yevethans began their campaign by attacking mining colonies in their cluster, which stirred the New Republic to intervene because the Yevethans had committed mass genocide on innocent settlements. During this conflict, Luke Skywalker had gone off with an adept of a faction called the White Current, an order that interpreted the Force in a diffrent light. The woman had convinced Luke that his mother was living with the White Current movement, but she needed his help to find the movement because they had been on the move to avoid the Empire. The conflict ends when Luke and a few other "masters" of the White Current create an illusion to make the small NR fleet look massive. At the same time, the Imperials who had origanally controlled the many Imperial vessels but were taken as slaves by the Yevethans mutinied and took the Imperial class ships back and hypered out of the system, taking the Yevethan crew and officers prisoner. This left the Yevethan fleet with only their own sphereoid light-class capital ships to duke it out with the now much larger NR fleet. The Yevethans would not surrender, and the New Republic had to destroy every last Yevethan ship.

After this last conflict, the New Republic has entered a period of peace and stability, with the only threat coming from the scattered Imperial warlords and small pirate and mercenary groups fighting from the fringe of the galaxy. Luke has re-established the Jedi order, and the war that has lasted almost forty years has finally ended.