'It's time to choose a side in this conflict... You can help President Cartwright by attacking the South or General Dee by advancing north. As hard as it may sound, you can also try to keep the peace with both sides. The one option I would strongly advise against is taking on both sides at once.'
The story quests you obtain throughout the Industrial Age map are significantly affected by the choice you make here. Some quests will occur in all of the quest chains, but others are significantly different with different rewards especially if you choose to not acquire any of the sectors by force. Many of the rewards for the peaceful route are larger than those obtainable through any war route. For example, when you finish this story quest line, if you have followed the war path, you'll receive 1 random blueprint and 20 diamonds (see Celebrate The Victory), while if you have follow the peace making path, you'll receive 1 random blueprint and 40 diamonds (See Celebrate the Peace).
War (if you acquire parts of New Cragshire AND Desperation by force)
Go North (if you acquire ONLY parts of New Cragshire by force)
Go south(if you acquire ONLY parts of Desperation by force)