ApostleCorp

"When JC Denton went into hiding, his compatriots founded ApostleCorp to continue his work until he was ready to return to the world. Tracer Tong, the infamous underground technologist, works as a lead researcher for ApostleCorp."

- Deus Ex: Invisible War description

ApostleCorp is an organization that has worked to create a new biological architecture thanks to nanites, that would be acceptable to all humans, and planned in the future to distribute these nanites worldwide to allow a perfect equality between human beings, the JC Denton's vision, a perfect democracy where everyone of equal ability connected (not assimilated) to the Helios AI. This has brought them into conflict with every other faction in the post-Collapse world, including the Illuminati, the Knights Templar, and to a lesser extent, the Omar.

History
Following the destruction of Area 51 and Majestic 12 and the beginning of the Collapse, JC Denton was unable to control the power of Helios AI, due to a defect in the nanite architecture, resulting in an imperfect merge. Before he loses control, he reveals his ideology of equality for all to his brother Paul and Tracer Tong. After that, his allies transported him to Antarctica, where JC erected a sanctuary for himself, using his newfound powers. Afterwards he fell into a prolonged coma, and remained in his refuge for twenty years.

Having the key to the future of the human species, Paul and Tracer Tong sought a way to wake JC from his coma, and found that the only way he would be restored was through the introduction of a new nanite architecture. In order to obtain this, ApostleCorp was founded by Paul Denton and Tracer Tong. Its purpose was to develop improved nanotechnology so that JC could complete the merger with the Helios AI and to awaken from his coma. The company also had to develop a universal nanite strain acceptable to all humans, and planned in the future to distribute these nanites worldwide to allow a perfect equality between human beings, JC Denton's vision, a perfect democracy where everyone would be of equal ability and connected to the Helios AI.

At some point, the nanites based on cloned Denton cells were tested on Paul, but his body violently rejected the infusion, so he had to be cryogenically frozen to save his life. After long experimentation, ApostleCorp managed to create a new type of nanite, a biologically-acceptable nanite, with the same capacity as the previous, but more polyvalent. This time, the process also involved changing the body physically at a biomolecular level, so the infusions were now compatible with the entire human population.

After this discovery, ApostleCorp created the Tarsus school program, which served as a field test for the new biomod architecture. The trainees would receive the universal biomod architecture along with the infusions at the end of their training. The Denton DNA upon which the nanites were based, would allow them to use the Black Gate teleporter and revive JC in Antarctica, as instructed by ApostleCorp.

The company had several enemies however, including the WTO and Order Church, two branches of the Illuminati created after the Collapse, which felt that the universal biomods threatened the Illuminati's power, and Knights Templar, a purist group bent on eliminating any and all forms of human augmentation.

Throughout the game, Apostlecorp is the only group that will not require Alex to kill anyone from the other factions. This is because, JC/Helios does not see the Illuminati or even the Knights Templar as enemies but merely as "topographies of ignorance".