After the Clone Wars erupted with the First Battle of Geonosis between the Galactic Republic and the Separatist Alliance, the 41st Elite Corps was part of the Grand Army of the Republic and was placed under the command of Jedi General Luminara Unduli, her Jedi padawan Barriss Offee, and Clone Commander CC-1004 "Gree." Early during the Clone Wars, Senator Padmé Amidala of Naboo was captured during the Mission to Rodia by Viceroy of the Trade Federation Nute Gunray and Separatist forces. After her droid, C-3PO, managed to contact a Republic clone trooper, the Venator-class Star Destroyer Tranquility was dispatched and ferried Green Company to Rodia. Green Company, led by Commander Gree, landed in Rodia's Senatorial Palace via LAAT/i gunships and arrested Viceroy Gunray after linking up with Senator Amidala, Junior Representative Jar Jar Binks, C-3PO, and Senator Onaconda Farr. After the arrest, Supreme Chancellor Palpatine thanked the senators and Binks for their help via a hologram set up by clone troopers, and dispatched supplies to Rodia immediately.
Green Company brought Gunray aboard a Consular-class cruiser from the surface of the planet to the Tranquility. General Unduli and Padawan Ahsoka Tano accompanied Gunray as security, and when the cruiser docked with the Tranquility, Gunray was brought to the ship's brig with the help of Senate Commandos so that he could be interrogated en route to Coruscant. Separatist forces, however, quickly created a strategy to either kill Gunray or rescue him, so that Separatist secrets could not be revealed. Separatist Head of State Count Dooku dispatched his assassin, Asajj Ventress, along with a group of Separatist light starships. After some time of interrogation, three Droch-class boarding ships and Vulture droid starfighters attacked the Tranquility. Commander Gree, who was alongside the Jedi and Senate Commando Captain Faro Argyus when they felt the attack, contacted a clone naval captain in the bridge requesting a status report. Upon hearing of Separatist engagement, Commander Gree deployed Green Company to repel Separatist boarders. The three boarding ships all successfully breached through the Tranquility's hull and deployed B2-series super battle droids to the hangar.
During the war, the 41st Ranger Platoon, a subunit of the 41st Elite Corps, conducted missions behind enemy lines to sabotage supply lines and vulnerable installations. During the Battle of Coruscant, troopers of the 41st Elite Corps were stationed aboard the Guarlara when it exchanged broadsides with the Separatist flagship Invisible Hand. During the broadside exchange, troopers of the 41st manned the cannons and many were killed when their stations were destroyed by Separatist fire, although the Guarlara was victorious from the broadside. Following the Battle of Coruscant, the 41st Elite Corps assembled at a Coruscant cruiser staging area as equipment and vehicles were loaded unto a Venator-class Star Destroyer and Jedi General Yoda arrived to command a sub-unit of the corps, the 41st Scout Battalion, before they were to be dispatched to Kashyyyk. 2b1af7f3a8