Koon was a senior commander in the Republic navy in 102 BBY, when tensions between the Jedi Order and Supreme Chancellor Signet Mezzileen had reached breaking point. Mezzileen had ordered the arrest of all Jedi and their Temple came under siege, but the Jedi were able to escape due to the incompetence of the Republic commanders. The Jedi fled to their base on Ossus and Koon was despatched with a fleet to crush the Jedi revolt.