As Neighorhood said, there is really no "end" to the game and the misson sets have their own ending. However many of the missions are linked together to tell a larger story.
Nation missions rank 1-6's Story leads into Rize of Zilarts story, and are required to be able to start RoZ missions. RoZ's story loosy leads to Chains of Promathia's Story, however none of RoZ needs to be completed to be able to start CoP missions. After clearing certain requirements, bonus missions/quests open up that lead you to the true end for RoZ and CoP.
The nation missions after rank 6 are completely seperate and have not much to do with each other.
Treasure of Aht Urghan missions also have nothing to do with the other missions and can be started at any time.