Completing the two main maps are the primary goal of the campaign, but the secondary goal of rescuing POWs is actually more important. Saving at least one POW from each sub-stage in an area will unlock that area's special POW bonus. These will boost various stats like AP gain, Sortie Points (energy), and much more – in addition to the normal upgrades you purchase from the base and unit Customization menus.
The process of how to rescue POWs is mysterious, with many early guides providing false information and speculation on how to increase your chances of rescuing. In truth, POW rescues are completely random. You might save anywhere from zero to three POWs in a single run, but the number won't be tied to anything you do. All you can do is grind the same mission repeatedly until your energy runs out or you catch 'em all. The fast-forward button at the top-right corner of the green will make the process go faster, and listening to TV, music, etc. while playing will reduce boredom.