Developer commentary in the Tumblr Q&A series reveals the following cut content:
According to narrative designer Mary DeMarle, the game was originally intended to feature Belltower's headquarters as well as a more extensive mission in Montreal. Cut designs for Montreal are also corroborated by other sources and concept art (for further information, please see the linked article for the city).
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...Our original intention was to enable players to learn more about Eliza and the Tyrants by exploring specific locations and finding books, emails, and/or characters who might be able to tell you more about them. But we needed to have locations in the game where it made sense to find this information, first. For a long time, we planned to have an entire mission take place inside Belltower headquarters – the most logical place to learn about the Tyrants. We also planned a more extensive mission in the city of Montreal, where you would discover a lot more information about Eliza. Unfortunately, late in production we realized had to scale back, and both of these locations got axed. By then it was difficult to find places where it made sense to uncover this information. So it ended up getting cut.
— Mary DeMarle
According to Mary DeMarle, the developers experimented with different quotes for the 12 game ending voice-overs: “We originally wanted to weave different quotes into all 12 voice-overs, but when we tried it, the endings sounded forced and formulaic. So we dropped the idea.”
According to developer commentary, "remote hacking and ATMs" were cut from the game. Further commentary states:
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The goal was to use the regular hacking system. However, any time you want to add something into the game, you need to account for more than the mechanics. Just for the ATM, we needed a model, textures, UI screens, sounds, etc. It doesn’t appear like a lot, but ultimately this translates into weeks of work which can be put to better use elsewhere. We also envisioned a system in which you could hack various accounts, with some accounts being linked to NPCs you’d encounter in the hubs. Putting something into a game is rarely an easy thing.
The dialogue system was designed to feature analysis of objects in the background, as something that could affect dialogue options:
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Some dialogs were supposed to feature objects hidden in the background that you could find and analyze in order to unlock blackmail attacks that you could use to convince people to give you stuff. Unfortunately, you had to do this while the character was talking to you, so you had to concentrate on 2 things at once, which meant nobody was listening to what characters had to say.
— Developer commentary (unsigned)
Hacking was originally designed to be more complex:
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The hacking was also supposed to be much more complicated than it is right now. Before accessing a device, you had to scan it for active ports. Some ports were slower but less protected, so you had to choose the best one for what you were attempting (whether you wanted to control or download something). Then you had to assign CPU cycles to various attack and defense programs while the system was trying to trace you. Anyway, we had it working in Excel and did three revisions before it was canned for the current node-centric system. People just didn’t get it.