By 40 ABY, as conflict broke out between Corellia and the Galactic Alliance, the Bothans soon became involved. Before long, Jacen Solo, now head of the Galactic Alliance Guard, began rounding up, interning and executing Bothans on Coruscant due to the support they demonstrated towards Corellia and the actions of the True Victory Party. When Bothawui joined Corellia militarily, Babo was one of the Bothan Admirals who became active in the Confederation military as an admiral, commanding part of the Bothan fleet at the Battle of Kashyyyk, engaging the Galactic Alliance Fifth Fleet.
After the battle, Babo met with Luke Skywalker, Tenel Ka, Han and Leia Solo, and Tojjelnoot. At first, he attempted to enlist the Jedi, Kashyyyk, and the Hapes Consortium into the Confederation, but he later agreed to consider the Jedi Coalition opposed to Darth Caedus—the former Jacen Solo—as neutral. He informed the others that the Bothans intended to assassinate Caedus, and requested that Skywalker and the Solos sanction the Bothan plans—which they did. Hundreds of these Bothan assassins were captured and detained by the Galactic Alliance Guard.