Story related. You will earn this on your Good Karma playthrough.
After absorbing the 7th and final blast core the next mission is "The Final Decision" which is the last in the game. Cole will start up the RFI only to find out it's true purpose before being stopped by Zeke. This is the final choice which decides which ending you play through. You're two female companions switch sides at the end, so siding with Nix and agreeing to power up and use the RFI is the Good Karma Choice and siding with Kup and agreeing to help the beast is the Evil Karma Choice.
This trophy will pop if you side with Nix for the Good Karma choice, it will pop after the credits once you are placed into free roam mode.
There have been reports that this trophy does not unlock properly if you skip the ending credits. If that happens, simply beat the game again (you'll be taken back prior to making your last decision end game) and sit through the credits this time and it should unlock.