Lightning successfully derails the Purge train out of Bodhum, with Sazh's help, triggering a massive response from PSICOM forces in the area. The security unit sends a Manasvin Warmech to subdue them, but it is defeated quickly. So begins the chase from the greater Sanctum as Lightning, Sazh, a boy named Hope, and resistance leader Snow stumble upon the remains of a fal'Cie sanctuary. Joining them is the mysterious Vanille, a girl whose origins are yet unknown. The four are selected as l'Cie by Anima, who gives them a Focus to complete. At the same time, they are labeled dangers to Cocoon society, fit to be destroyed.
Some time later, the l'Cie manage to infiltrate the city of Palumpolum, each with personal objectives. Snow and Hope are waylaid by an Ushumgal Subjugator before reaching the Estheim residence as the others continue to evade PSICOM around the city. They eventually meet with Hope's father to plan their next moves, but are cornered by a Havoc Skytank. Though a particularly long battle, the Skytank is also dispatched.
Fang, a l'Cie working with the Cavalry unit of the Sanctum, safely guides Lightning's party out of Palumpolum, but soon after, they find Vanille and Sazh captive aboard the Palamecia, and must escape again. Their escape vehicle crashes into ruins identified as the Fifth Ark, whereupon the party encounters Fang's former superior, Cid Raines, himself turned l'Cie by the Sanctum and set on obliterating the party. He too is cut down.
Meanwhile, Fang's shoulder begins to burn, releasing the eidolon Bahamut. Her trial is about to begin.