Query on War and Peace

As part of a discussion elsewhere, I posed this question and now would like to include it here should any have an opinion. The more I learn, the more I understand.
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Regardless of the justifications for war, I don't see how peace could ever be one of them for peace is a distinct opposite of war. Yet it is the human majority's desire to exist in peace. I say majority for there are always those who aren't happy unless there is chaos and strife.

Someone tell me how peace can be gained when you instigate a fight to protect one man and his way of life and in the process kill his brother. We are by nature going to protect what is ours as a mother protects her child, a husband protects his home, and a nation protects its citizens and way of life. Even some would say that is no justification for violence but instinct dictates that we act instead of remaining passive. Passivity is not a natural instinct for fight or flight is the norm. It takes cowardice or personal control to avoid that instinct.

But my question involves peace. How can peace be attained by waging war, regardless of the reasons, and while creating allies you also create enemies? What difference does it make if you have one enemy or thousands when that one can generate as much dissension as the many whether it be today or in future?

In looking at the entire war situation, justifications are made.....right or wrong...and we are at the mercy of the political machine. Society being what it is, there must be leaders and guidelines put into place to govern behavior. When those guidelines are determined worthy, all leaders should have to follow them and not be allowed to deviate from them for personal purposes or national.

Certainly, as nations, each creates its own guidelines by which to govern but the nations do not stand alone but make up pieces of a whole which encompasses the globe. When the nations come together in agreement on terms by which all should govern as a united alliance, it behooves each nation to live up to that agreement. When a country (or its leader) determines that it has justification to break that agreement does that make it right? Should that nation assume a continued alliance by default of its inclusion to the agreement when the other countries have called that nation into question and the nation is thwarting the guidelines which were put into place to maintain some semblance of order and peace worldwide? Regardless of a just war theory as a basis to determine the validity of or justification for waging war, the "UN Charter has carried forward the idea that all wars that are not fought in self-defense or with the approval of the UN Security Council are illegal wars." Of course, in one instance of war, the UN backs a country. In another, there becomes a division.

We are left to determine what is fact and what is fabrication and, in looking beyond the bias of some media, irrefutable fact can be found to support the cause of war or to condemn it. How do you support a cause which causes the deaths of innocents? I realize that determining the innocents within modern warfare can be risky at best for the person actively fighting. It is the leader who puts his man into the field to have to make those determinations on a moment's notice. I do not call into question the soldier who does his/her duty and should be respected for putting his/her life on the line and for living up to what being a soldier entails. Who I call into question is the leaders and/or government he answers to whether out of duty, respect, love, or fear. However, war should be a last alternative and gravely considered by all those who oversee and protect us lesser-powered individuals who make up the general populace of the world. By all means, defend and protect, but do so against the targeted person (Hitler, Hussein, bin Laden, or whomever) and with consideration for those who inhabit the space with him, their culture, and for the overall effects upon us all.

When you fight under a guise of defense against terrorism, please explain to me how the measures used may inhibit the creation of more cause for that terrorism and hatred?