Quoting Light Mars
Is this the third time Kira has been captured? I'm losing track, JK.
She was captured once during the first attacks on Eden as part of the initial group of test subjects, but escaped. Later, while the Crown was gathering survivors from the Wastes to be test subjects, she and her group was captured. This time, she was taken because the Crown realized they weren't going to win this battle, so they took her as a prisoner of war for bait.