Yeah, it's the only downside for making a long branching story with arcs and tons of characters, every ending is a beginning.
That said 2 of the games I'm working on now ( Zero One and Writing destiny) have their own ending just like this game and at the same time they add to the main story ( for example Zero One has information about what happened to ''Zero'' after she became a normal human), The reason I chose to do that is because the main story is nearing its end and the final game in the series is approaching faster than I expected.