As of the sequel, Deus Ex: Invisible War, all of the possible endings are at least partially canonical. The canon "decision" is for JC to merge with the Helios AI in the "Benevolent Dictator" ending, but the merge is unsuccessful. This still results in the failure of Area 51, a technological blackout, and the death of Bob Page regardless. In this way, the results of all three endings, if not the choice behind them, are somewhat canonical.
The Benevolent DictatorEdit
Requirements: Deactivate the uplink locks, engage the primary router and proceed to merge with Helios.
Cutscene: JC Denton speaks with Helios, is convinced to merge with it, and proceeds to rule the earth as an omniscient, objective, absolute ruler.
|"If there were no god, it would be necessary to invent him."|
- Deus Ex: Invisible War establishes this ending as the most canonical (though the merge is unsuccessful and eventually results in events similar to the other two endings as well).
New Dark AgeEdit
Requirements: Cut the coolant flow to the antimatter reactors, disable the failsafe mechanisms, and activate them to initiate a meltdown event.
Cutscene: Area 51 is destroyed by the massive blasts, cutting world communication networks and destroying both Bob Page and Helios. This thrusts the world into a technological blackout, but also frees it from media control by the Illuminati.
|"Yesterday we obeyed kings and bent our necks before emperors. But today we kneel only to truth..."|
|— Kahlil, Gibran|
- Deus Ex: Invisible War establishes this ending as at least partially canonical, with the Helios AI/JC Denton merger inadvertently resulting in Area 51's Destruction. Communication and globalization are still able to return in the medium-to-long term, however, as seen in Invisible War. In addition, the Illuminati is shown to persist even following following the Collapse.
The Invisible HandEdit
Requirements: Neutralize the four blue fusion reactors, trigger the Infusion Control Switch, simultaneously destroying Helios and killing Bob Page.
Cutscene: JC Denton and Morgan Everett discuss plans for the future in a world where the Illuminati rules unopposed. This shows JC is at least complicit in their plans, if not actively collaborating with them.
|"Better to reign in hell, than serve in heaven."|
|— Paradise Lost, John Milton|
- Deus Ex: Invisible War establishes this ending as partially canonic, though it is arguably the least canonical. Helios is clearly shown as still existing in the sequel, and on top of that, JC is fused with him, further contradicting the possibility of an Illuminatus JC. On top of that, the eventual destruction of Area 51 would serve as a massive blow to their power and influence.
In an hour-long narrated playthrough of Deus Ex with Sheldon Pacotti and Chris Norden, Warren Spector noted how he originally wanted a fourth ending to be possible in the game . This fourth ending would allow JC to side with Bob Page and Majestic-12, presumably destroying Helios and killing Everett. This is mentioned around 49:20 in the YouTube video.
Some evidence of this ending still persists in the final game, with Page at one point pleading with JC by offering him total control of Europe (this would apparently have been a serious option had the last ending been included). This corroborates some rumors which have circulated since the game's development, which suggest that originally Deus Ex would have included a second "MJ12 Loyalist" path to completion, which was later scrapped. The reason for the omission of this fourth ending is as of yet unknown.