I think you could take this as a seat of the pants issue, and just be a discovery writer. Write your book. Keep your notes, as you have, disconnected or not. Do not focus on the future until your story is fully written. Not necessarily fully polished, but you have a coherent start, middle and ending.
THEN assess your world and your characters. Is there another story in this setting? Does it involve the same characters? Is there another quest that is at least equally important, either for them, or for a next generation or alternate set of heroes?
You will still have time to modify your current story to allow leeway for another story, you can tweak it that way, or hint at the next story in some scenes. Leave some unanswered questions that would be setup for the next book.
But concentrate first on writing the best story you can, so IT gets published, and then see where you finally are. Don't mess up your mind by trying to think of a whole series at once.
As far as the current story goes, I wouldn't save (or transform) the universe in book One, it leaves you few places to go for book Two, except saving the universe again. That's just me, not a blanket admonition. Buffy the Vampire Slayer got away with an excellent new apocalyptic threat every season for many seasons, but I personally would find doing that much more difficult in book form.