Set a decade after the events of its predecessor, the Galactic Republic is on the brink of civil war, with thousands of planetary systems threatening secession under the leadership of a renegade Jedi. Meanwhile, Padmé Amidala, now a Senator, narrowly escapes an assassination attempt. The Jedi Council assigns Obi-Wan Kenobi to discover the assassin's identity while his apprentice, Anakin Skywalker, is tasked with protecting Padmé. As Anakin guards and spends time with Padmé, he begins to develop deep, conflicting emotions for her.

Obi-Wan's investigation leads him to a distant planet, where he uncovers a secret clone army being created for the Republic. His search further connects the assassination attempts to a separatist movement led by a mysterious figure. Anakin's assignment to protect Padmé takes a personal turn as he grapples with his duty to the Jedi Order and the intense feelings that challenge his commitment. Amidst political machinations and emerging dangers, both master and apprentice find themselves drawn into a web of intrigue that will test their loyalties and the very fabric of the Jedi philosophy.