The Navy served Skywalker and Kenobi at the Battle of Sullust to destroy a Separatist ships. The fleets were also in the battles of Christophsis, Ryloth ( Blue Squadron), Malastare ( Red Squadron), Rishi moon, and the Second Battle of Geonosis (Red Squadron).
Skywalker, Tano, and Koon would later lead Shadow Squadron to destroy the Malevolence, the newly discovered superweapon, with the assistance of Jedi Knight Obi-Wan Kenobi's forces. The two found Jedi Master Plo Koon, Commander Wolffe, Sergeant Sinker and clone trooper Boost. After losing several ships and their crews, including Jedi Master Ares Nune and Commander Kite, Jedi Anakin Skywalker and Ahsoka Tano went out looking for any survivors of a secret weapon. The ship came under attack by Separatist forces, causing Yoda and his squad to make their way to the escape pods and Zak and his ship to escape the area. The Republic Navy sent a small shuttle with Jedi Master Yoda, commanded by Commander Zak. The Navy sent ships to Teth after the 501st Legion was pinned down.
