The combat system isn't 100% done yet - I'm taking some time to properly iterate it, so the details are somewhat in flux.
The current version I have puts you in control of the MC, with one selected girl as a support fighter, and allows you to select your "squad" of soldiers who you will fight with. The girl will provide passive bonuses as well as a random activated ability (eg. Hana will give you a passive boost to HP and DEF and a random chance for a massive boost to ATK) and the squad will alter what moves you have available to you and will work better or worse against other troop types.
I might extend the system to allow multiple squads to fight at the same time, but at the end of the day CK is a visual novel built on a visual novel engine and you can only push the system so far before it snaps like a twig :P