The Second Battle of Bothawui occurred a week after the first one did. Since Trivas did not have a ground invasion force with him, he was forced to orbit Bothawui and pick off the ground forces. After a week, the army arrived from distant Ni'novia and began their landing. While he waited for the army's victory, Jedi Master Jason Altor arrived with an overwhelming fleet.

Knowing he was outmatched, Trivas called Lord Kracor to divert most of the fleet preparing to attack Falleen to Bothawui. With his interdictor still running, Altor's fleet was unable to hyperspace in at close range. The Galactic Alliance fleet was forced to travel in realspace for twenty minutes before reaching the waiting Sith forces. While they were traveling, the Sith reinforcements arrived behind them.

Even though the Sith had two fleets, the Galactic Alliance fleet was larger. Instead of allowing himself to be surrounded in a slugging match, Altor turned his fleet around and drove through the Sith reinforcements. This move allowed the Sith fleets to merge and maintain a defensive formation around the planet within range of the interdiction fields.

On the planet, the Sith forces managed to drive the Galactic Alliance defenders out of the capital city and into the mountains. With the Sith fleet preventing the Galactic Alliance from landing reinforcements, the Sith were nearly in control of the surface. Despite this, Trivas knew that if he could not hold the space, the ground army would be slaughtered by the superior numbers of the Galactic Alliance reinforcement army.

Instead of smashing two massive fleets together, both Trivas and Altor agreed to meet on an abandoned station orbiting the planet. There, they drew up a basic cease fire with the outlines for a more permanent treaty to be discussed later. This treaty was the groundwork for the Treaty of Ruusan that was signed a week later.

As part of the agreement, the Sith would retreat from Bothawui without causing further destruction. This was the last major battle of the Galaxial War.