1. The main quest has four "A" endings, "Sea", "Land", "Sky" and "Breakthrough." However, the quests needed for "Sky" and "Breakthrough" wont appear until after you've finished another "A" ending (or possibly "B" ending) like "Sea" or "Land." Just like the Takeda Assassination in Sengoku Rance, once you've beaten the game by "Sea" or "Land," you can go back to a previous save and the quests for "Sky" and "Breakthrough" will appear retroactively.
So in other words the first time you beat the game you must be on the "Sea" route (easier) or "Land" route (more difficult). Then you go back to a turn 10 or turn 11 save and beat the game with "Sky" route (if you want or need to beat the game on a different route).
On the 1st page of your Achievements collection, you can see all the endings. The top four are "Sea" route, "Sky" route, "Breakthrough" route and "Invasion" (land) route.
2. In addition, the game has a 2nd Quest which is unlocked by achieving 5 sidegoals during "A" route playthroughs. You don't need to do all 5 sidegoals on the same playthrough- if you miss one, you can unlock the achievement later in a different "A" route playthrough. You can see these sidegoals on the bottom of the 2nd page of your Achivements, with the "A" in the title.
The five sidegoals are-
- Four nations survive
- Defeat Kaybliss
- Save Hornet
- Find the Soul Transfer Center
- Pope wish wasn't used (the Pope is Crook Mofus)
Once you have these five sidegoal achievements unlocked, you'll be able to start 2nd Quest games.