In a nearly vacant town, R2-D2 and his team find a clone commando suffering from amnesia.

Clone trooper Tup succumbs to a mysterious mental illness that results in the shocking death of a Jedi Master. Unable to account for his murderous actions, Tup is sedated and sent back to Kamino for examination. Meanwhile, Admiral Trench of the Separatists informs Count Dooku of the betrayal, and is convinced that the killing stems from something deeper. Anakin Skywalker and ARC Trooper Fives accompany Tup, but their return trip is ambushed by Separatists.

While Jedi Mace Windu and Obi-Wan Kenobi lead an attack against the Separatist forces on Anaxes, the Bad Batch and Anakin Skywalker infiltrate an enemy starship to ensure a Republic victory.

The Siege of Mandalore begins, and Ahsoka turns to Anakin and Obi-Wan for help.