As you should already know, Vanguard Bandits consists of 20 Chapters, made up of 56 different Missions, depending on the decisions you make throughout the game. In addition, there are 3 main "branches" to the game, and 2 endings in the Kingdom and Empire branches. The chart and information below should help guide you in the right direction, and get you to whatever missions you want to play. Or if you've already started and you need a kind of "checklist" to see what you're missing, this chart and the information should be helpful to you as well.
Okay, I KNOW it's horrid looking; but it gets the job done.
Now, you see the numbers encased in circles that appear on the chart? Those are where I have marked off important decision points; areas where you will be forced to make a decision, and the consequences will have an effect on how the rest of the game plays out. Below is a list of all the decision points, what they mean and what each choice does. Match the number of the decision up with the number on the legend, and there you are!
1: After defeating the last opponent in Mission 3, and only if Bastion's Level is 8 or higher, a choice will come up. The options are "We must attend to *someone*" and "I shall find that murderer!". If you choose the first choice, you will stay on the Kingdom Branch and move to Mission 4, but if you choose the second choice, you will move to the Empire Branch and Mission 25.|
2: After you have completed Mission 5, a messenger from a certain nation comes to address you and asks for an audience with a certain someone. A choice will come up; the options being "Actually, Zeira, I'll meet with him.", and "... ... ...". Choosing "... ... ..." will take you to Mission 7, choosing "Actually, Zeira, I'll meet up with him." will bring up another question, the options here being "Yes. Tell him I will depart soon." and "I'm afraid not." Choose "Yes. Tell him I will depart soon." to head to Mission 6; choosing "I'm afraid not" will take you to Mission 7 instead.
3: During Missions 6 and 7, if Bastion's HP is reduced to zero, you'll move on to Mission 9. If Bastion survives and you complete the mission, you move onto Mission 8.
4: After completing Mission 10 or 11 (Chapter 8), and ONLY IF YOU HAVE COMPLETED THE GAME ONCE AND HAVE SAVED CLEAR DATA AFTER THE ENDING, you'll be given a choice. Choose "I intend to end the war" to go on to Mission 12, as usual. However, if you choose "I will conquer the Continent!", another question will come up. Answer "I will conquer the Continent!" again to move onto the Ruin Branch, and Mission 45.
5: After completing Mission 14 (Chapter 11), there will be an additional scene if you completed Mission 9 on this playthrough. If you did complete Mission 9, then Nana will join your party in the Bahamut ATAC.
6: After completing Mission 18, assuming that Bastion's level is less than 20, you'll be given a choice. Choose "Of course, Milea. I would be honored." to have Milea join your party in the Amphisia ATAC, or choose "I'm sorry, Milea, but I can't do that." and she doesn't. But why would you do that to cute little Milea? 8)
7: After completing Mission 22 (Chapter 19), the game analyzes the morale of everyone in your current party and determines the average. If the average is higher than +7, you will go to Mission 23, but if it is +6 or lower, you will head to Mission 24. Mission 23 is the good ending, Mission 24 is the really, really bad one.
8: After completing Mission 38 (Chapter 17), the game analyzes the morale of Sadira and Cecilia, comparing them. If Sadira's morale towards you is higher, then you head to Mission 39 and the Sadira ending. If Cecilia's is higher, you head to Mission 42 and the Cecilia ending. To get the ending you desire, keep the girl who's ending you want as happy as possible; when choices come up, make sure you choose what the lovely lady wants to hear, and if a certain someone asks you to keep a secret and you want her ending, choose to keep it!