How To Get The Second "True" Ending:
Destroy ALL buildings and survivors during missions and SOS missions. Also, you must destroy the colony shaft completely during the fifth and final SOS mission in the game. Afterwards continue onward as normal. Tyrant will be your final boss. After defeating Tyrant, go to the MOUNTAIN.1 stage and you'll recieve the bad ending.
Note: This can be done on any difficulty level.