Both of my comics include a war.
In my comic, True Power, it takes place as a war was ending and a treaty was being made. The country has two ruling powers (the Council and the king). The Council was in favor of continuing the war, the king was not so they had the king sent to Earth along with some of his allies and thus the main story of True Power takes place.
In the sequel, True Power: MS2, it's now many years after the treaty has been completed and the two countries are living mostly peacefully. The countries may be at peace, but individually they don't get along.
The reasons for the war were religious disagreement and went on for about 400 years.
In my comic, Celestial Chronicle Shion, the people of Earth came into contact with aliens. As earthlings worked on creating space travel to go say hi and visit them, the aliens came without warning and attacked Earth first. The humans don't know why they are being attacked by them outside of "they want to enslave us" (in the comic, the main character, Shion, has learned more of the reasons why, though not quite everything). In the story, it's been 61 years since the war started so it has been going on a couple of generations now.
heh...