Collapse

Following the events of Deus Ex, JC Denton merged with Helios. However, Helios has made a fatal error in judgment in selecting JC alone for the merger. While extremely advanced, JC Denton is simply not equal to the task of containing the AI on his own. He handles it for a while, but before long, Paul Denton and Tracer Tong have to put JC in stasis in Antarctica where his enemies will not find him. The global network is not necessarily taken down, but it is severely damaged.

The Illuminati then move in, but as Morgan Everett said, they do not do anything directly. Chad Dumier forms the World Trade Organization, and Nicolette DuClare forms the Order, revealing herself to her followers only as Her Holiness, never revealing her identity. These two groups stage a conflict, but in truth Chad and Nicolette work for the Illuminati, and eventually fall in love.

Meanwhile, Tong and Paul found ApostleCorp, with the goal of bringing nanoaugmentation to the masses. Their ultimate goal is to augment the entire populace, creating a perfect democracy - and distributing Helios among the masses, thus relieving the strain on JC alone, and Helios ruling based upon the will of the majority.

In an interview, Warren Spector said that he wanted to choose one of the three endings in Deus Ex to build Invisible War upon, but later included elements of the other two. So while the Helios ending is the true canonical ending, elements from the New Dark Age ending are used (the merger eventually leads to the Collapse) as well as the Illuminati ending (following the Collapse, the Illuminati move in and take over. So while the player can choose not to merge with Helios at the end of the first game, the sequel is based upon that choice being made, and the repercussions of the other two endings as well.