That sounds alright to me. My basic idea was that they would get kidnapped and taken back to the enemy empires idea of a POW camp. There they would be questioned, violently if your okay with that, and then basically left with the other prisoners. 
Our characters would then have to devise a way to escape(I have a bit of a plan for this as it will also be part of my characters development.) and then either we help topple the enemy empire somehow or do whatever we please now that we have no one telling us what to do. I'm open to your thoughts on how the story can proceed after that.