I betrayed Alia and solved the ghost mystery and now all the Rebels are dead and only Rats are in the Ederneum outpost. Where's everybody at? Nothing happened when I assault the final dungeon (On the good route, a cutscene would happen at the forcefield entrance in Level 4) and before I knew it, I beat the final boss without any conclusion to that plotline.

Don't worry. At that point, you can even kill everybody and still beat the game. I did just that; killed everybody everywhere, on purpose, before raiding Akbaa's final lair.