Right, so im looking for an japanese style animated film i saw a long time ago some time between 2004 maybe to 2008. 

it sort of the style of Jin-Rou : the wolf brigade. but it was a bit more digitally done from what i remember. 

anyway, all that i can really remember is a couple of fragments for example. 

I remember a group of soldiers dressed similar to the wolf brigade in jin-rou, and they had entered a cave like enclouser (maybe blasted their way in unsure) and there were a ton of sack like things on the ground (maybe like large eggs?) and the soldiers started to shoot them. 

well after they had done that they all started to leave. for what ever reason one solider stayed for a minute staring around, he noticed a human girl like hanging out of one of the egg things and he was going to shoot until he noticed it was a human, long story short he ends up adopting this young girl without anyone knowing about it passing her off as his daughter, later on it turns out shes the key to driving some huge space ship or base or what ever that can move and fight but only a certian blood line or something can operate. she ends up being forced to pilot this thing and fighting another one just like it i think? but the thing is the big ship thing is also a city that tons of people live on.