This game does close off the story of Estelle and Joshua, but there will be dangling plot threads that remain unanswered to be taken on through 3rd and the other games later on. The series is still going, with the Japanese games at the sixth game- all telling a continuous story between them.
- Endless History: A Falcom News Site - http://www.esterior.net - - http://www.sanctuarycrew.com | http://www.eidenyaku.com -
To add a bit (or a lot, this is me talking) of detail to the above, this series uses individual story arcs in the service of its continuous narrative.
FC and SC form the Liberl arc, with SC resolving all major questions left outstanding at FC's ending. The teo games were originally planned as a single entry split for technical reasons.
The 3rd has it's own largely self-contained story (albeit building directly on SC's conclusion) which resolves some of the minor outstanding plot threads, develops some characters further and includes a ton of world building for future games. Basicslly, it's a bridge game that has payoffs in each of the games that follow it and will undoubtedly continue to have payoffs in future games.
Zero and Ao form the Crossbell arc. The location is new and the focus shifts to an entirely new cast with their own stories. Certain major elements in Zero build off of SC/The 3rd and there are special appearances by Liberl arc characters both major and minor. The game can be played on it's own if you don't mind losing the emotional impqct of certain scenes. Ao on the other hand wraps up the arc but does it in a way that requires knowledge of all the previous games if you want to make sense of things. It also has a nasty quasi-cliffhanger ending where everything is resolved but still leaves a ton of unanswered questions. This leads directly into...
Sen no Kiseki, which begins the Erebonia arc. Again, new location and cast but appearences by certain recurring characters and lots of references to past games, being the game they've been building up to since FC. It runs concurrently with Zero and Ao and makes sure you know it. From what I've heard (I'm about 2/3rds in) it has an ending that makes a bit more sense if you've played previous games and features the biggest, most evil cliffhanger yet. The sequel is presumably coming out next year on the franchise's 10th anniversary.