The world is now ruled not by Illuminati, not by MJ12 but an AI, Helios, a merge of Daedalus and Icarus, one that has no ambitions, prejudice or emotions. J.C Denton's merging plays a crucial role in that Helios understands human emotions or needs without being one himself.

INVISIBLE WAR SPOILER

The aftermath :
In Invisible War, JC Denton's merge is revealed to be incomplete hence he is kept in stasis. Alex Denton revives him with his biomod architecture. With the merge being complete, JC Denton is practically a Universal Constructor, able to control weather and alter anything at an atomic level. If the Helios ending is chosen, the Aquinas protocol is used to distribute nanites across the world linking every human with Helios and bringing forth a Utopian age.

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