The film opens just a few days before the beginning of Star Wars Episode III: Revenge of the Sith. Anakin and Obi-Wan are on Alzoc III with Captain Rex and Commander Cody fighting the Separatists. The two generals decide to split up, with Anakin going North to take control of the mountains while Obi-Wan heads to the droid outpost. After taking control of the place, Cody tells Obi-Wan that the Jedi Council wants to talk to him, so they establish a communication with the Jedi Temple. Mace Windu, Plo Koon (in hologram), Ki-Adi Mundi, Saesee Tiin, Agen Kolar and Yoda are in the War Room of the Temple. When Obi-Wan’s hologram appears in the room as well, to the master Jedi’s surprise, Ahsoka is there (in hologram).
Ahsoka reveals that the Mandalorian resistance is falling apart and Darth Maul is destroying everyone who stands against him, but with the help of the Republic they could win the planet back and Korkie Kryze (who became the leader of the resistance) promised they would join the Republic if the planet is freed from Maul. Obi-Wan asks how Ahsoka ended up on Mandalore and she reveals that she found some Mandalorians on Chandrila who remembered her from her adventures on Carlac and asked for the Jedi help, She thought their cause was good and decided to go help them. Mace Windu explains they don’t have many troops available so Obi-Wan proposes to send a part of the 501st Legion, since the Battle for Alzoc III is almost over.
Windu agrees but asks Obi-Wan not to reveal the truth about the mission to Anakin. Obi-Wan agrees despite not liking the idea. On Alzoc III, Obi-Wan returns to the moutain with Cody and joins Anakin, telling him a part of the 501st Legion has been assigned to free Mandalore. Anakin proposes to go but Obi-Wan explains the Jedi Council orders are only to send the Clones. Anakin appoints Rex at the head of the group that will go to Mandalore. Rex takes Jesse and Kix with him too and he contacts the Bad Batch, asking them to come help them too. On Mandalore, Ahsoka and Bo-Katan, along with the former Mandalorian cadets, are hiding at the ancient Academy that is not used any more.