Deus Ex was originally intended to be three-to-four times biggerin terms of content while in development. A large number of ideas were either scrapped or not fully implemented due to time constraints:
Warren Spector's original pitch (to Electronic Arts), "Troubleshooter", involved a security specialist who could use different solutions for hostage situations, covert missions and more. The concept was shelved for several years because the technology wasn't available to make the concept a reality, and Spector eventually moved from EA to Looking Glass Studios, where he began to experiment more with the idea (renaming it "Shooter"), resulting in moving to ION Storm and commencing the project.
There were many scrapped level concepts early in development, including missions set in Siberia, London, Los Angeles (post-earthquake) and even the Moon!
A plotline (scrapped early in development, but had voiceovers done for two cutscenes) allowed the player to stay loyal to UNATCO, hinting that there could have been a seperate storyline in which you continued to hunt down resistance forces. It can be seen here.
There was a scrapped level concept in the Hong Kong section where JC would find a slave trader in Old Canal Road. He would be able to board the slaver's boat and free the slaves (as one was mission-critical), but would be attacked by MJ12 troops while escaping.
The Vandenberg plotline was intended to be completely different, and involved two factions (the Raiders and the Salvagers) constantly fighting each other to gain control of the base. Gary Savage was originally intended to be betrayed by Howard Strong and killed, with the player finding his body in the radiation tunnels below the facility, and his daughter (Tiffany) agreeing to help if JC promised to get revenge on Strong. This plotline would have culminated with JC fighting one of the robotic spider-bots in an arena. There was also a scrapped subplot between Strong's son, Ned, and Tiffany.
In tandem with the White House level mentioned below, there were a series of planned levels revolving around "Mt. Weather", an underground bunker in Virginia where government leaders would be placed by FEMA to ensure continuity of government.
The optional encounter with the Morpheus AI in Morgan Everett's home was originally intended to have a built-in text parser, which the player could use to interact with the AI in a limited fashion.
At one point, the developers discussed having a unique death scene if the player dies in Area 51, as well as an additional ending for players who wanted to side with Bob Page in the final mission. It was scrapped due to time constraints.
Early betas had different inventory and hacking options. Instead of the visual framework seen in the final version, hacking a camera showed a DOS-like menu that allowed the player to change a turret's tracking noise, change the perspective of the camera and more, and the HUD had a different framework. Likewise, it was possible to not only change J.C.'s skin color and hair, but also his clothing as well.
There is a large amount of Dummied Out code still in the game (some of which is restored by the Shifter mod):
On JC's first version to Hell's Kitchen, it was originally possible to access a phone message in Paul's apartment from his girlfriend, which hinted at his NSF loyalties. The Shifter mod restores this content.
JC could originally access a (fully-voiced) VOIP conversation between Tracer Tong and Juan Lebedev, where they argue over whether or not to bring JC into the conspiracy.
Textures are present for the scrapped "White House" level, which supposedly involved JC going to meet the President and his wife and getting advice on what to do.
In the Hong Kong section, there is an Red Arrow Triad NPC (normally inaccessible due to being placed outside the level boundaries) that makes reference to Maggie Chow having had a relationship with Paul Denton. Whether this was actually part of a scrapped plotline or just Chow trying to throw JC off her trail isn't confirmed.
In the final game, Ford Schick disappears after you rescue him from the MJ12 sewer laboratory. However, he was originally intended to appear back at Smuggler's hideout, where he thanks the player for saving him, gives an augmentation upgrade and has several lines discussing the effects of the Grey Death. The Shifter mod also restores his content.
There is an unused "Departure" musical cue for Area 51 in the music files, which likely would have tied in with the original intention to have the lunar base level be featured directly after it.
Ion Storm Austin tried - unsuccessfully - twice to create a Deus Ex 3 after the release of Invisible War, but both attempts never got off the ground, for a variety of reasons:
The first attempt, Deus Ex: Insurrection, went through several different design ideas and concepts. There was one for an Interquel where the main character was a soldier who had seen the destruction of Area 51 in the original game and later became a black-ops member working for the President to stop Illuminati agents. Another idea had a foster family who worked for the CIA as the main characters, and they were all working to stop an unmentioned conspiracy. Another was set after Invisible War and would have canonized the JC Denton ending, and would have followed his brother Paul as he worked against his brother's interests. Ultimately, the team tried to develop a concept that was a Prequel to the first game (following the exploits of JC's father, Blake, who was affected by alien technology and worked to stop a Chinese invasion of the U.S.), but the project was never realized and was abandoned when Warren Spector left Ion Storm.
Soon after, there was another pitch brought forward for the then-untitled "Deus Ex 3", which was to be developed by a different internal team and would have been an open-world cyberpunk game. Like Insurrection, the player would assume the role of JC's father, except this time they were a failed clone who was literally thrown out in the trash and forced to become a mercenary in a futuristic New Orleans to make ends meet. It would have allowed the player to "flatline" characters (momentarily render them dead) to access their memories and learn more about the world, as well as have randomized missions. The project got as far along as design documents, but competing egos, budget cutbacks and the closure of the Austin office rendered the project dead.
Eidos Montreal considered the idea of creating a Montreal hub in Deus Ex: Human Revolution, though it never made out of the concept stage. The intention was to create an unique look with housing areas built up of triplexes with wrought-iron spiral staircases. Singapore and Upper Hengsha were also considered. The latter was even partially implemented and one of the most impressive (visually and conceptually) elements of the game. Unfortunately, it had to be excised due to time and budgetary constraints, like many, many other elements.
The beginning level would had been Adam breaking into Sarif industries with Megan as Mission Control. The fact that you were breaking into Sarif and not into a competitor industry would not be revealed until the end of the mission. The end would also have a conversation boss fight with Megan, that would give detail about their failed relationship.