The Holy verse says:
"And fight in the cause of Allah and know that Allah is Hearing and Knowing." (2:244) When you read the verse lets first notice the following:
1- The verse is mentioning "Fighting" NOT "Attacking" or "Conquering" which means that Muslims here are fighting an army NOT innocent civilians, because "fighting" in this context means "fighting" in a war and this is how it was used throughout the Holy Quran.
2- This "Fighting" should always comply with the rules of "Jihad" explained before. The first rule is that it is a war against those who ATTACK the Muslims not an aggressive act initiated by the Muslims. The proof of this is another verse in the same chapter that says: "Fight in the way of Allah those who fight you but do not transgress. Indeed. Allah does not like transgressors." (2:190)