The I'm-going-to-bed-in-five-minutes version is that like Pioneer 1, Pioneer 2's government is completely inept and fucks everyone over in the quest for power. The ending is total nonsense as is Endu. Endo? Enkidu...? Endthedupes. Endthedupes is some mashup of Rico and Flowen's will given physical form to kill IDOLLARS who currently takes the form of the "germ/great shadow." Other endings, aren't. I think all endings ultimately result in P2 landing to screw over another planet. In something of a kicker, P2 declared independence from Coral prior to EP3, so they are probably really fucked now.
While most characters do have their own semi-interesting stories, they don't really get resolved and they usually just say thanks for listening (and give you a card iirc.) A good portion of the folks on the hero side get screwed. Kranz actually dies and is then cloned, so Sil'fer becomes even more annoying while FOmarl (I'no?) loses her mind since that was her childhood crush. Arkz are supposed to get their revenge for reasons and ultimately don't, managing to only kill Kranz (lol.) The leader of the Arkz formed the group to take revenge on Pioneer 2 for using his dead daughters as experiments. Like everything else involving the D-cells, that went real swell and they end up getting away (becoming the final bosses before the Germ.) As for the hero side, well they are run by a real fat fuck who is annoying and generally only exists to tell you where to go.
ST apparently did not understand their own tools very well, because they never really put out anything after launch to expand the story.