Deus Ex 3 was in development at one point after Invisible War came out, and before Human Revolution was even a thing.
A recent presentation by Joe Martin at VideoBrains, explored one of the least talked-about aspects of game design; a game's deleted scenes, or in this case, a whole game.
Martin has worked as a games journalist and games writer for various publications, and in his presentation he brings up Deus Ex 3, a game which was in development at Ion Storm, the same team who had previously worked on the first two games.
The image above shows two of the possible plots that would've been included in the game. The game would've been set before Invisible War.
"The first is about an augmented Black Ops soldier who goes AWOL upon discovering he’s been used for dodgy dealings. His handlers find him and threaten him with either court martial or his wife’s execution if he doesn't do one final job. What’s interesting is that the missions would have fluctuated between flashbacks and new stories," says Martin.
"The second story begins immediately after the ending for Deus Ex in which you destroy all global communications. In this story you’d investigate the collapse and try to save your sister from a cult which arises in the chaos."
The rest of the presentation is well worth a read. In it, Martin goes over how design ideas from that game affected design and narrative decisions in games like BioShock and Blacksite: Area 51.
There is also a whole segment about legendary designer Warren Spector, who's work includes the original Deus Ex, Thief 3 and Epic Mickey, and how his work with designers like Richard Garriot, Ken Levine and Harvey Smith shaped their future games.