By final faction(s) do you mean Chaos, Synergy and Cycles? If yes than those factions are gates. They are impossible to beat and don't have a technology tree. For the storyline, despite it being a but messy, due to how the quest system works in the game, the storyline is error proof. If works for hundreds of people, so perhaps you are doing something wrong? The quests that drop Apocalypse armor plates spawn with around 20% when you explore a new node ( system ) above 130 ly.