Quarter: What happens after you get to Paris till the end of the game?
*** OBVIOUS SPOILER IS OBVIOUS *** JC eventually meets with Illuminati leader Morgan Everett, and learns that the Gray Death virus was intended to be used for augmentation technology, but Majestic 12, led by trillionaire businessman and former Illuminatus Bob Page, was able to steal and repurpose it into its current viral form. Everett recognizes that without VersaLife's universal constructor, Majestic 12 can no longer create the virus, and will likely target Vandenberg Air Force Base, where X-51, a group of former Area 51 scientists, has built another one. After aiding the base personnel in repelling a Majestic 12 attack, JC meets X-51 leader Gary Savage, who reveals that Daedalus is an artificial intelligence (AI) borne out of the ECHELON program. Everett attempts to gain control over Majestic 12's communications network by releasing Daedalus onto the U.S. military networks, but Page counters by releasing his own AI, Icarus, which merges with Daedalus to form a new AI, Helios, with the ability to control all global communications. After this, Savage enlists JC's help in procuring schematics for reconstructing components for the UC that were damaged during Majestic 12's raid of Vandenberg. JC finds the schematics and electronically transmits them to Savage. Page intercepts the transmission and launches a nuclear missile at Vandenberg to ensure that Area 51 (now Majestic 12's headquarters), will be the only location in the world with an operational UC. However, JC is able to reprogram the missile to strike Area 51. JC then travels there himself to confront Page.
When JC locates him, Page reveals that he seeks to merge with Helios and gain full control over all nanotechnology, essentially becoming a god. JC is contacted by Tong, Everett, and the Helios AI simultaneously. All three factions ask for his help in defeating Page, while furthering their own objectives, and JC is forced to choose between them. Tong seeks to plunge the world into a second Dark Age by destroying the global communications hub and preventing anyone from taking control of the world.[28] Everett offers Denton the chance to bring the Illuminati back to power by killing Bob Page and using the technology of Area 51 to rule the world with an invisible hand.[29] Helios wishes to merge with Denton and rule the world as a benevolent dictator with infinite knowledge and reason.[30] The player's decision determines the course of the future, and brings the game to a close.
source: wikipedia.