On Aargonar, Bultar Swan fought alongside Jedi Master Ki-Adi-Mundi, A'Sharad Hett, Bhat Jul, and Anakin Skywalker. Aargonar itself was an insignificant planet, but it lay on the border between the Republic and Confederate armies, and thus represented a strategic vantage point in the war. Under the command of Ki-Adi-Mundi, the Republic forces faced a setback when Master Hett's command ship was shot down stranding the Jedi Master, Bhat Jul, and Anakin Skywalker behind enemy lines. However, the Republic could not afford to retreat as the had previously at Jabiim, and Master Ki resolved to ensure Aargonar was not lost to the Confederacy. Bultar Swan and the Republic were eventually victorious on Aargonar as Master Hett and Anakin Skywalker used their position behind the droid armies to trap them between Master Ki's and Bultar Swan's forces.

During the war, Bultar Swan also led a squad of clonetroopers in an attack on a heavily guarded Separatist fortress on the planet of Amaltanna. Kilometers of durasteel and shields strong enough to withstand orbital bombardment made the fortress all but impregnable. Single-handedly, Bultar Swan infiltrated the fortress and slowly made her way past automated weaponry and security droids in an attempt to locate the Separatist minion hiding within. As Bultar Swan drove deeper and deeper into the fortress, the Separatist minion locked herself behind stronger and stronger security mechanisms. But Swan's intentions were not to get at the Separatist minion. Rather, Bultar Swan used the fortress against her trapping her within and destroying the life-support systems.

At the end of the war, the Separatist launched a desperate attack against Coruscant led by General Grievous. During the invasion, Bultar Swan piloted a Jedi Interceptor to battle the Separatist fleet. The battle saw the death of Count Dooku and seemingly brought and end to the Clone Wars. However, it was simply another step in Darth Sidious' plan to take over the galaxy. Not long after the Battle of Coruscant, Darth Sidious issued Order 66. Bultar Swan was at a medstation tending to wounded soldiers when the clones turned against the Jedi. The Jedi healers were able to warn Bultar Swan who managed to survive and go into hiding.

Months later, Bultar Swan managed to make contact with Jedi Master Tsui Choi and the two rendezvoused on Eriadu. On Eriadu, Bultar Swan informed Master Choi that she had been in contact with other survivors who planned to meet and make plans to deal with the Sith. Convincing Master Choi to attend, the pair left to join the other Jedi on Kessel. The meeting was organized by Jedi Knight Shadday Potkin and the attendees included Roblio Darte, Sia-Lan Wezz, Ma'kis'shaalas, Koffi Arana, and Jastus Farr.