Happy Wars

To unlock all story missions, you must have a rank of 26 or higher. I recommend leveling up to rank 30 if you are having trouble beating some of the missions. Most missions are rather easy and straight forward, but there are two missions that seem to give people trouble in particular. These two missions are "War of the Worlds!" (4-2) and "The Final Battle" (6-2). I have included tips on both of these below that should hopefully help make these missions much easier for you.

War of the Worlds most people have a major issue with the AI allies because they tend to be very stupid and make choices that will make the mission an annoyance like constantly destroying the bridge to the enemy castle. To avoid this problem entirely and to make this mission a breeze, choose to play as a Cleric. When the level first starts, take the right path instead of going straight like the rest of your allies. Follow this path until you get to the enemy castle, and then build a cannon. Once it is built, shoot the castle gate from a distance until it is destroyed. Do not attack the gate from up close or else a lot more enemies will spawn. 

Here is a video that should help those having difficulty:

The Final Battle choose to play as a Mage. Make sure you have the Cosmic Wand equipped as well as Marshal's Hood. Both of these items are rewards from previous levels in story mode and are great items. Then, after you defeat each wave of enemies, go to a side of the castle. The melee enemies will come after you so defeat those when they come. Then, take care of the remaining mages at a distance if possible and take care of them one by one.

This video may be helpful if you are having difficulty: