
After Thrawn became an admiral, he was sent with the Imperial Fleet to go put down an insurgency on the planet Batonn. Nightswan proved to be Thrawn's intellectual match and a brilliant military commander in his own right. Throughout his early career, he hunted a mysterious operator named "Nightswan", who he later found out had been orchestrating many of the rebellions across the galaxy, many of which would eventually come together and form the Rebel Alliance.

Thrawn himself was primarily tasked with capturing pirates and putting down rebellions in unstable sectors. The two of them became close friends and used each other's own strengths to help the other rise to the higher echelons of the Empire. It was during this time that he met Governor Arihnda Pryce, an aspiring businesswoman and politician hoping to claw her way up to the top. The Imperial Admiralty came to despise him, trying to use every opportunity they could to have him discharged, but after each court martial he came out unscathed, even being promoted to commodore after one of them. With help from his aid, translator, and fellow officer, Eli Vanto, Thrawn quickly moved up the ranks, gaining recognition for his unorthodox but effective military tactics. Thrawn used this new development to his advantage, and infiltrated the Imperial Navy, posing as a loyalist to the Empire, but truly only doing it for his people and not the Emperor, who he knew was actually evil. Most unexpectedly, the Emperor gave Thrawn a naval commission. Thrawn was able to win an audience with Emperor Palpatine, and, in order to ensure a possible alliance between his people and the Empire, Thrawn offered to give Palpatine astrological information of the Unknown Regions, as he deducted that Palpatine had an interest in the region. Sure enough, a Star Destroyer visited the planet after several months and Thrawn was discovered by the captain. Thrawn selected a planet in Wild Space as his spot of "exile", as he knew that it was on the edge of the Galactic Empire. In order to do this, Thrawn was formally exiled from Chiss space for military insubordination, although this was all staged in order to publicly explain the absence of one of the Ascendancy's highest ranking officers.

Out of love and a fierce loyalty towards his people, Thrawn selflessly volunteered to venture off into Imperial space in order to assess their military might and see if they would make a good ally to help defend the galaxy from what the evils on the outer regions of the galaxy.

At some point, he and his people discovered a threat looming in the Unknown Regions of Space. Somewhere in the Outer Rim, Thrawn came into contact with Anakin Skywalker, and would ultimately come to hold the man in high regard. He was part of a scouting force to go search for possible allies by the time of the Clone Wars. Thrawn started out as an officer in the Chiss Ascendancy Expeditionary Force, the navy of the civilization from which he came, and loyally served in it as a commander for many years.
