1. You have uploaded the Aquinas spec to the Templars and allied yourself with Luminon Saman.
2. Three Illuminati elite troopers will attempt to block your exit from UNATCO HQ. JC Denton messages his intent to kill you.
3. The Templar Paladins outside UNATCO will not harm you. Head past the south docks and witness the Paladins and Illuminati battling each other. You'll find a mag rail and two energy cells here.
4. Continue through this door to the east side of the island.
5. Make your way to the Templar encampment in this bunker.
6. Talk with Saman and he elaborates on his plan: to unleash nano predators that will end biomodification and preserve the purity of the human species.
7. This unlocked trunk holds three ammo clips, an EMP converter and a spiderbomb. To the right is an energy blade and three more ammo clips. A medkit is in the northeast corner.
8. Return to the island's west side to this building near the statue entrance. Inside are three ammo clips, an EMP grenade and a medkit. A cloak/thermal masking combo will keep you concealed while you climb onto the roof.
9. Time to ditch pacifist play. This rooftop position affords you some cover as you pummel the ApostleCorp forces below. My preference is the rocket launcher.
10. Now you must kill Paul and JC Denton. Knocking them unconscious is insufficient to complete your goal. My preference is the rocket launcher's alternate fire, which launches a slow-moving missile that you can guide while in flight. Fire several rounds into each Denton to kill them.
11. Cloak and activate your thermal masking to avoid detection by any remaining grays or turrets. Step into the infusion chamber and activate the Helios uplink machine.
12. A cutscene plays of JC Denton reviving as a mortal.
13. You receive a new goal. Kill JC Denton - AGAIN!
14. You should still be cloaked and thermally masked. Head back to your rooftop position and once again use your rocket launcher's alternate-fire to bring JC down. Several rounds should do the job.
15. Reactivate your cloak/thermal mask and start the Helios uplink machine once more.
16. The final cutscene plays of unseen crowds cheering the words of Luminon Saman.
17. Lastly, you are left with this quote from John Bunyan. Game Over.