Brionac loses track of Yulie's whereabouts after the Eulalia is destroyed, but catches up to the party once they reach Platapana Passage. Coincidentally, this is immediately after Jude tells Gawn who they're running from and he takes off. It's likely Gawn tipped them off.
Which might explain why he didn't just fight the Kraken back in the Cerulean Tunnel. He knew the party would be passing through there any moment and didn't want to risk blowing his cover.
Also some situational irony as to Gawn's fate: He's the mysterious 11th member and trump card of Brionac, a revelation that helps them finally capture Yulie. He himself gets trumped by Gungnir's 11th missile where there were only supposed to be 10.
Jude boards the Silver Star Express alone, but when he's ambushed by soldiers, the rest of the party suddenly shows up to help him. It may look strange, but remember that Yulie has a couple of teleportation spells, namely Replace and Gather. It's possible that she used a variation of Gather on Jude's position, or just switched the party with another group of soldiers using Replace!
Occurs to the party at one point near the end of the game - "If this is a prison... where are all the prisoners?".
It's meant to occur to you, the player. Think about what 78 years of war with technology of a level 20 Minutes into the Future from 2010's would do to a planet and the people living on it.
