Volvox

I'm playing this game for the first time. I just destroyed Wargoth asteroid and i was unsure what to do next, so i saved game and pressed Fast Forward. I skipped all missions just to check what will happen. Soon Reticulan warship crashed and i had to help them. I didn't want to do this mission so i skipped it waiting for research to complete. Soon reticulan mission was canceled and instead of just Game Over, there was rebelion on Laputa. My question is - is there a branch in story and what will be diffrent?