Here is some thoughts that could be included in Adventures in Polaris Universe:
There could be a civilization that have for some reason survived or evolved in the surface, and the same goes for underground, caves and space.
The players could discover a large autonomous cave that might even be the "hollow earth" and go across the globe as a network of tunnels and large open spaces. This area could contain a civilization of fantastic creatures that have existed as they are even when the humanity resided on the surface.
The players could discover technology that is biblical or mythical in origin, or instructions for such devices. In india, there could be traces of Devas, or what they left behind in middle-east, there could be traces of the Arc of the Covenant and so on.
There could be a mysterious captain with his rumored ship "Nautilus" which stalks seeming invisible on the ocean floor. Sometimes a smaller mini vehicle is launched from inside this ship to port on any stations, but the ship itself is never seen on a port. There could be many mysteries resolved around this captain and this ship. The captain might have always had this ship, even while the humans lived on earth or this ship might have been acquired in some way. The ships evades all normal and supernal type of detection and is invisible to the eye.
Of course, the rumored Atlantis could be discovered, and other ancient technology not necessarily related to what is mentioned on the book.
There could be a crossover to Cthulhu myths, the players could discover R'lyeh, the deep ones, great
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ones and so on. This could even launch cataclysmic events on a larger scale that would threaten the humanity under the sea as a whole and force unision or at least actions on a grander scale.
A crazed cult or individual who is convinced that all of the Corals in the planet must be eradicated, and that the Coral is indeed responsible for the demise of human race.
I will also introduce new systems to be used in campaings:
The first is an idea called PROLOGUE, where the players must freely conversate how their character came on as a group and to tell a short story what their characters have accomplished together before starting the campaing. This act is known as PROLOGUE and each player participating on it is awarded with 5 EXP that may immediately be used on the character before start of the first session.
The second idea is INDIVIDUAL GOALS, so that each player must state at least three individual goals on their characters. When a character manages to accomplish one of these goals they are rewarded with 10/20/40 exp and the third goal is also seen as the end goal on that character.