So, the Lucifer has arrived, and Earth's final hour has come.
No, wait, in a cunning plot twist, the Terrans have replaced Earth with a giant, floating, cardboard cutout of Earth! Surely the Shivans will be fooled by that...
But alas! Exposure to vacuum has deformed the cardboard cutout so much that the shivans see right through this cunning deception, and go looking for the real Earth...

Hmm, Journey of a thousand Miles:
Nothing obviously wrong (except for the buggered starfield, which looks somewhat ugly when compared to the mvp one), but one thing should be considered: Its first stage starts off with the "Subspace" loading screen, the other three do not. Breaks the mood a bit, IMHO.
Also, a custom load screen for the last part would be really cool.
While we're on the subject of mood-breaking: Skulls and Bones? Why would the refugees put skulls and bones on their ships? Consider this a bit of fridge logic.