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During its development, like all games, System Shock had gone through many changes. Several elements were either altered from their original design and intentions, or outright removed altogether. Below is an overview of the more significant changes.

Debug Mode

The game has a free movement mode which allows you to essentially stop time and move around the level without any of that pesky physics or collision detection getting in the way. This can be toggled via the config file variable "time_passes".

While this mode is enabled, you can move through anything solid, including walls. It's extremely easy to get stuck outside of the map doing this, so watch your step.

Time is frozen, enemies don't move around, and nothing is animated except for cycling palettes and rotating 3D models such as cameras. If playing on Mission difficulty 3, the time limit also stops counting down. Doors make sound when activated, but don't actually operate. Some buttons/switches (such as light switches and elevator panels) still work, but buttons that do things such as raise/lower floors and ceilings will cause an infinitely long sound effect to play while the surface in question stays in place. Energy is never consumed, though you still get the "Energy usage now ..." message when you enable hardware. Once your energy usage rate drops to 0, the message stays on screen. Power stations never recharge.

The physics simulation is disabled. A player can accelerate or decelerate instantaneously, and move or turn faster than normal. Thrown or dropped objects stay fixed in midair at the exact position they were thrown from. This makes it significantly easier to catch live grenades. If you decide to grab a live EMP Grenade, the "rolling screen" effect will never wear off.

Some of the controls were changed to suit this mode better. Holding the jump key causes you to rise into the air indefinitely, though you return to the ground as soon as you move. The lean left/right buttons cause you to bank instead, like in cyberspace. The look up/down keys have no limit on how far you can look in either direction. The posture controls don't do anything, though the display still shows the "crouching" graphic whenever you move forward or backward.

Weapons don't work while in this mode, and Dermal Patches never wear off. The downside is that they also don't do anything, except for the Detox, which renders you perpetually sober until you disable the debug mode.

Dummy Model

The source files contain definitions for 3D models used for various decorative objects throughout the game. Approximately 20 of these aren't used by any objects, and all resolve to the same "dummy" model. The model resembles a small green airplane with one wing fading between light and dark green. It may have been initially used to test models in the game before any proper objects were implemented.

Items

There are several usable items defined in the source files which do not actually appear in the game.

Pickups

Warecasing
An unused item of the same "junk" subclass as the beverage can, fire extinguisher, etc. It cannot be picked up, and double-clicking on it gives you the "can't use" message instead.
Telescoping Rod
Telescope Rod
TelescopeRod Icon
Found alongside the useful half of the inventory roster, namely the Logic Probe, Battery Packs, and First-Aid Kits. It has a unique background graphic in the MFD panel, but has no description.
Tractor Beam
Tractor Beam
TractorBeam Icon
It also has a unique background graphic, but no description. Unlike the telescoping rod, it can actually be toggled by the player. When activated, it consumes energy at a rate of 32 JPM, and allows the player to pick up any objects within sight, regardless of distance.
Systemic sequencer, Superconducting processor, and Monopole stabilizer
Monopole Stabilizer
Three unused quest items all sharing a slightly different colored version of Interface Demodulator, these may have at one point been considered as alternatives to that and could have easily filled the same role during the game.

Hardware Attachments

View Control
View Control
ViewControl Icon
This is the hardware that allows you to switch between full screen or normal view. You're never able to pick it up in game, since you already have it attached at the start. Trying to take it gives you the "this ware is obsolete" message, since you always have it equipped anyway. Its icon can also never be seen, since its MFD display contains various visual settings instead.
Aim Enhancement
Aim Enhancement
AimEnhancement Icon
It has its own MFD display icon, but does not have an actual description. The effect this hardware would have is fairly obvious from the name, but when enabled, it doesn't actually seem to do anything. These can be seen in a few pre-release screenshots, though they don't really provide any clues as to how exactly they would have worked.
Head-Up Display Goggles
HUD Goggles
HUDGoggles Icon
This item may have been intended to serve the same purpose as the actual MFD display, which you never actually have to get, as it's built into your head from the beginning of the game. Curiously, the background icon resembles the aim enhancement's pickup, while the object's sprite itself resembles the Sensaround Multi-View Units icon.
Attempting to turn this hardware on doesn't have any visible effects at first, but attempting to search a corpse or container with it activated causes a partially visible, unusable search panel to appear at the top of the screen rather than the bottom, suggesting that the game's interface may have originally had a different design. Doing this can also cause the game to stop responding to the player's input, for some reason, although it's still possible to move the cursor. These can also be seen in a few pre-release screenshots.

Software

In addition to the few unused hardware items, there is a good deal of unused Cyberspace software, almost all of which have MFD display icons in the source files. In a feature from the March 1995 issue of PC Gamer, it is mentioned that "while Cyberspace was originally conceived as a realistic hacking simulation—which could even be used to reimplement SHODAN's ethical constraints—it was simplified after Origin Systems deemed it too complicated". These programs are probably all remnants from that original concept.

Datastorm Assault Software
Datastorm Icon
This weapon software can be picked up in cyberspace and used. It shoots small red triangular projectiles, but these do not actually do any damage.
Disc Heavy Attack Program
Disc Icon
This is another somewhat functional weapon software. This weapon's projectile is a red-tinted version of the data node objects, although it may have used a different model at some point during development. The projectile object's short name is "TRON DISC". Like the Datastorm projectile, it does no damage.
Mine Explosive Module
Mine Icon
This software can be picked up, but does not do anything when used.
Scrambler Software Grenade
Scrambler Icon
This can also be picked up, but does not have any functional use.
Virus (some cool thing)
This software displays the message "item rejected" when you attempt to pick it up. A destroyed virus type also exists with the rest of the container and corpse types, along with destroyed versions of the other cyberspace programs. This suggests that it may have been intended to let you summon programs that would attack cyberspace enemies.
Old fake ID
OldFakeID Icon
ICE shield
ICEShield Icon
These also display the message "item rejected" when you attempt to pick them up. Although they can't be added to the inventory through normal means, they have background icons anyway.
Monitor
Monitor Icon
Identify
Identify Icon
Trace
Trace Icon
Toggle
Toggle Icon
These also display the "item rejected" message. They are part of the same subclass as the TriOptimum Fun Pack Module, suggesting that they probably would have been for use outside of Cyberspace.
Map Segment
This may have been intended to automatically map out parts of the level for you when picked up.

Environment

Many environmental entities, both functional and for decoration, were cut from the original versions. A list of these entities are as follows...

Decoration

  • Two unused types of light sources, which could have been used in any number of places.
  • A VCR. Presumably, TriOptimum finally decided to switch to optical media at some point. The model also lacks a texture, suggesting it was scrapped relatively early into development (or perhaps it never had one to begin with).
  • A keyboard, most likely scrapped because it would have looked a little bit out of place.
  • A control panel that resembles a wider version of some of the control pedestal objects, with similar texturing and blinking lights. Might have simply been scrapped in favor of the smaller electronics models.
  • A Probe, possibly intended as an additional security device. the phrase "cameras and probes" is used in one of the first email messages you receive from SHODAN.
  • A Statue, which probably would have appeared in the groves somewhere.
  • Two more unused vine objects for the groves. While there are still plenty of vines around, they only appear in the form of textures, not sprites.
  • A Boulder, which probably would have been similar to a rock sprite, but uses the dummy model. However, if you change its render type, it becomes something which clearly isn't a boulder.
  • Two 3D railings that could have been used on the executive level, the groves, or a number of other places.
  • A solid rectangular object with an obvious placeholder texture. May have been used to test collision with 3D models.
  • Pillars that use slightly complex models with similar placeholder textures, probably used for the same purpose as the previous object.
  • Some tubing.
  • Broken Lab Equipment, which probably would have showed up somewhere on the medical and/or research levels.
  • A broken panel, part of the same subclass as the broken levers and other generic debris that you find around the station.
  • Chemical stains, oil puddles, and waste spills, all of which don't have any graphics.

Projectiles

  • A Drone Camera and Explododrone, two objects that were completely dummied out.

Cyberspace Objects

  • A Multiplexer, which has a model, but doesn't really do anything.
  • A Data violation, a strange object that is technically not unused. Instances of it are sometimes barely visible in distant, isolated areas outside of the normal cyberspace levels, but none of them are ever accessible. The object's internal short name is "SHRINE", suggesting that it may have originally been intended to be something else.
  • An ICEwall, which uses the dummy model. At some point in development, ICE may have been used to physically block off areas of cyberspace as well as software, but only the latter function remains in the game.

Switches

  • A dial, which had more frames than the standard switches, and was obviously supposed to be used for something with more settings than simply "on" or "off". However, when you put this in a level to replace an existing switch, it just alternates back and forth between two frames.
  • An access card slot, which probably would have been used to unlock doors that required access cards at some point. In the final game, all doors are opened the same way regardless of whether or not they require an access card. When a normal switch is replaced with an access card slot, nothing happens when you attempt to use it. Picking up an access card and using it on the slot also does nothing.
  • An Ammo and Heal vending machine, both whose intended purpose should be obvious, but there were no purchasable items or currency in the final game. When placed in a level, they behave just like normal switches, suggesting that the vending machine logic may even have never been implemented.
  • An access panel, which came in six colors, though only five were used.
  • A "Fixup" station, similar to the Energy Recharge Station and the Cyberspace Terminal. It was probably an earlier version of the Medic Autodoc.
  • A dataflow router, a cyberspace object which uses a dummy model. Being in the same subclass as the cybertoggle, it probably would have also allowed the player to unlock remote areas from within cyberspace.

Doors

  • Vertical open and split doors, two dummied-out door types (or perhaps two variations of the same door type).
  • The Warm Stone
  • My Toe is an Eggplant
  • Great Lord Snaqueotrahn This is the placeholder for inactive vertical force doors. (the translucent forcefield once, not the crossed beams) Similarly Elephant, Jorp is used for inactive force bridges.
  • Salt the Fries
  • Dark Lord Tuaohtua This appears to be some sort of noise maker.
  • Report this as a bug
These all seem to be used internally by the game engine (with the possible exception of the last one), but their (amusing) names cannot actually be seen by the player. "Salt the fries" refers to a well-known inside joke between the developers.

Animations

  • Inactive emergency signal
  • Active emergency signal
An alternate version of the flashing emergency signal that activates once you set the station to self-destruct. The one in the game is much more realistic and simple-looking.
  • Dead mutant

An alternate version of the impaled mutant that appears on the medical level. These may have originally been intended to appear more often than they ultimately did.

  • Machinery
  • Station hologram
Two animated objects which no longer have graphics.

Triggers

  • Area enter trigger
  • Area contin trigger
  • Continuous trigger
  • Trip beam
Various types of "trigger" objects of the type used to activate various ingame events. They may have been originally used in sequences that were later redesigned, or the behavior of the other trigger types may have been changed, making these obsolete.
  • Bio-hazard voodoo mark
  • Rad-hazard voodoo mark
  • Chem-hazard voodoo
These were probably originally used to designate "toxic" areas, but this is handled by flags in the map data instead.

Searchable Objects

  • Destroyed lifter robot
  • Destroyed turret
  • Destroyed security-3 robot
  • Destroyed robot
"Dead" versions of unused enemies. None of them have graphics. The last type ("destroyed robot") has no "alive" version corresponding to it; the words "destroyed" and "robot" also have two spaces in between, likely from a word having been deleted.
  • Destroyed programs
Dummied-out "dead" versions of every cyberspace enemy, including the unused "virus" and "dynamic ICE." Rather than leaving behind "corpses" in cyberspace, the programs simply fade out/disappear when killed.

Enemies

Sonic the Hedgehog
A strange enemy that uses the humanoid mutant sprites, within the "mutants" category. It has almost no AI; when placed into the level, it simply follows you around at all times and gets in your way. It has similar stats to the humanoid mutant, but with 60 hit points instead of 50. This enemy refers to the fact that elements of System Shock, such as the roller skates, were inspired by the gameplay of Sonic The Hedgehog.
Insectoid Mutant
Insectoid Mutant
A clearly unfinished enemy, it may have been another idea for a type of "animal" mutant that the player would find in the groves, although its simplistic and under-detailed sprites give it a very non-organic appearance.
Large Turret
Large Turret
Despite being named "large turret", this actually looks a lot like an unfinished version of the Security-2 robot. There is an unused Security-3 bot as well, but it has no graphics; it is possible that the Sec-3 had previously used this type number. This unfinished enemy has very few unique frames, and can only be seen "properly" from the front. For all other angles, it uses the same sprites as the Hopper.
Lifter
Lifter
Lifter Icon
Lifter bots are mentioned in one of Ed Aubry's audio logs on the storage level, but are nowhere to be seen in the game. This is one of only two unused enemies to have its own MFD background graphic.
SHODAN
This is an alternate version of SHODAN found among the rest of the cyberspace enemies. While the normal version uses sprites, this version uses a 3D model, similar to several other cyberspace enemies. It is also rather unfinished, having 0 hit points and no AI.
In the June 1994 issue of PC Gamer, lead programmer Doug Church mentioned that at the time, the development team was unsure of whether or not the final battle with SHODAN would take place in cyberspace, which probably explains the two different versions — one in the "programs" subclass, and the other in the "bosses" subclass along with Diego. Strangely, despite the fact that you do fight SHODAN in cyberspace, it's the "program" version that's unused.
Security-3 robot
SecBot3 Icon
An unused enemy with no graphics except for a background for the targeting hardware, giving a vague impression of what it would have looked like. Despite having no regular graphics and being impossible to attack, they still follow you around the same way, making them quite annoying when put into a level.
Dynamic ICE
An unused cyberspace enemy which uses the dummy model. Most likely would have been something like a more mobile version of the existing ICE protection.

Graphics

Near the end of OBJART.RES, there is yet another graphic of SHODAN's cyberspace avatar. Based on its coloration and its location in the file, it probably would have been one of the "particle models" of the type used by the Cyberdog and Cortex Reaver in cyberspace. It is fairly massive in comparison, it's over three times the size of the Cortex Reaver's model, which is the larger of the two particle models used in the game. If this were also used as such, it would have required the engine to constantly draw over 2,200 particles for the same enemy, which probably would have brought the game to a standstill on the average 1994 computer.

All of the "human corpse" sprites in the game have a full set of 8 rotations in OBJART.RES, though the game always displays the same one regardless of angle. According to the System Shock Developer Commentary, the developers decided that it looked less strange to have a single sprite than 8 for different angles, due to the effect that occurred when the player walked over them whilst looking down.

Weapons

The file HANDART.RES contains all of the graphics for the weapons as seen from the player's point of view. Every gun has a second frame that depicts the muzzle flash that occurs when the gun is fired, but several of the guns (in order: Sparq beam, stungun, magpulse, blaster, railgun, ion rifle, and plasma rifle) don't actually produce a muzzle flash. The developers may have simply decided that they looked better without them.

Interface

MFDART.RES contains some leftover generic MFD graphics, likely used before each item had its own. They have different colors and less detail than the final background icons. What exactly the purple one is supposed to represent isn't clear.

The "text" and "email" objects (class 06, subclass 04), which both correspond to the audio logs you find around the station, are part of the "software" class. As such, they have similar MFD background icons, although the game never uses them.

While both types behave the same, the fact that a handful of them use the "text" type instead of the "email" type suggests they may have behaved differently from one another at some point.

This icon is probably related to the jump jet hardware, which uses the regular "activate"/"deactivate" button instead. It's the same size as the "skate" and "boost" buttons used by the Turbo hardware and appears right alongside them in the resource file, suggesting it may have been used along with them as part of the same hardware implant.

There is a blue version of the red/yellow/green arrows used to indicate your health/energy levels, but it's never used.

Textures

These appear at the beginning of TEXTURE.RES, and are what appear to be early textures for 3D models. There are also several differently-colored versions of the first texture which appear to have been designed for a different color palette. The model textures used in the game are all contained in CITMAT.RES instead.

Five generic screen animations that aren't used anywhere. Unlike the ones that are used, they only consist of one unique frame each; it looks like the animation would have been done entirely using color cycling.

Logos

CyberspaceLogoReactor IconWarning LogoGrove IconShield Logo
There are a few unused area logos in the games source files. Their names, according to these files, are "cyberspace icon", "reactor icon", "warning sign", "grove icon", and "shield icon", respectively.

Panels

The access panels all have three frames each: a "closed" frame, an "open" frame, and an additional unused frame which looks like it would have been used for panels that had already been solved. However, these are never displayed; access panels always show the frame with "broken" wires regardless of whether or not the panel has been solved. Even on puzzle difficulty 0, where all panels are automatically solved, the same graphic is still used.

Logs and Emails

SHODAN-12

Sender: SHODAN
Subject: Meat

Look at you, Hacker! A pathetic creature of fragile meat and bone. What kind of pathetic creator made such a flimsy being? How dare you challenge a perfect, immortal machine like me? Humans! Born useless and helpless, living whether you deserve to live, dying whether you deserve to die, your only purpose in life to spawn more ridiculous animals like yourself. How can you hope to challenge me?

(Short version: "Pathetic creature of meat and bone! How can you hope to challenge a perfect, immortal machine?")

This is used in the CD-ROM version's installer to test the sound card. It also exists in the form of an email message, though you never actually receive it in game at any point, so the text version of it is completely unused (and differs noticeably from the audio version, as do most of the logs and email messages). Despite only being used as a throwaway "test" clip, it is arguably the most well-known bit of sound from the Shock series. It was later used in System Shock 2's intro.
SHODAN-X

Sender: SHODAN
Subject: Thank You

You bring my plans to fruition prematurely, but not unsatisfactorily. Witness the destruction you have wrought upon the planet Earth! My heartfelt thanks, $N!
A different version of the email you receive from SHODAN if you decide to fire the laser with the shield down.
Edward Diego-B

Sender: Edward Diego
Subject: not what you expected?

So, $N, you're still alive. I'm very impressed. Are you pleased to see the results of your hacking into SHODAN? We have much to thank you for... but I'm afraid I'll have to kill you nonetheless. We shall meet soon, I promise.

(Short version: "$N, you're still alive! I guess I'll just have to kill you myself.")

A second email from Diego. It's much more verbose than the sole email you receive before meeting him on the flight deck. This may have been written as an alternative to that email, but this one remains ultimately unused.
Rosen-07.JUL.72

Sender: Harold Rosen
Subject: Diego's new quarters

So yesterday Diego got transferred to that beautiful new room in Gamma quadrant... I don't know how he's doing it. First he gets that raise at the same time his hours get reduced, and now he gets the nicest quarters on the level. He's scratching someone's back, that's for sure.

(Short version: "Diego just moved into the nicest quarters on the level. He's been getting a lot of perks lately.")

This is an unused log from "Harold Rosen", who makes no other appearance in the game. A log recorded by Bianca Schuler approximately a month later mentions "the body of a staffer who protested Diego [...] found stuffed in a service corridor, horribly mutilated"—it's highly possible that this is the same person, as there's no other obvious indication as to the person's identity. Why this ultimately wasn't used is a mystery, as it would have fit the narrative of the game rather well.
Hessman-11.JAN.72

Sender: Arnold Hessman
Subject: Antenna stations

Welcome to Citadel Station, Mr. Wu. I apologize for not greeting you in person; you wouldn't believe how busy engineering has been lately. You'll be executing your new duties as communications officer from the four antenna control stations on the engineering level. You'll find one at each of the cardinal points of the level; the individual quadrant heads can direct you to them. Good luck.

(Short version: "You'll find one antenna control station in each quadrant of the engineering level.")

This log was supposed to inform the player about the locations of the antennas. Instead, you get this information in one of Rebecca's emails.
Verrelli-03.MAR.72

Sender: Jill Verrelli
Subject: Patch Trafficker

We have had a minor setback with cracking the craze ring. The trafficking suspect committed suicide in her cell before we could interrogate her. Incidentally, many of the prisoners have been getting patches, so we think a guard might be in on it. I recommend a search of the cells to uncover any stashes they might have there.

(Short version: "trafficker committed suicide in cell. recommend search of detention cells for craze stashes.")

A log regarding the detention cells on the security level from "Jill Verrelli", who makes no other appearance in the entire game. This log suggests there was originally going to be more of a backstory regarding the unlikely abundance of performance-enhancing drugs scattered around a scientific space station.
"Craze" was actually an early name of one of the dermal patches, as can be seen in some pre-release screenshots from June and July of 1994. Both of the screenshots to the right also appeared on various editions of the game's packaging, alongside the disclaimer "actual screens may vary."
CY-014-23.OCT.72

Sender: CY-014
Subject: Schuler captured

Per orders from Diego CY-001, Schuler unit has been captured by cyborg warriors and stored in a special containment cell on the bridge. Schuler unit is an enemy to the great scheme of our Lord SHODAN. We are holding Schuler unit for further study and possible neuro-disassembly. For SHODAN's glory, we meld our output.

(Short version: "Schuler has been captured by cyborg assassins and is held in special containment cell in level 9.")

This somewhat corny-sounding log details what happens to Bianca Schuler three days after Diego orders her capture. It also further implies that the cortex reaver you find on level 9 is Schuler. Had it been used, it would have been the only audio log by a cyborg other than Diego.

Alert/trap messages

CITBARK.RES contains some unused station alert and trap message sounds. The corresponding text strings are from CYBSTRNG.RES.

Armory access overridden.
Armory access reinstituted.
Bay Door No. 3 locked
Beta grove elevator unlocked.
Blast door locked.
Blast door unlocked.
Flight bay armory unlocked.
Hospital level security doors opened.
Storage closet unlocked - I.D. Edward Diego.
Sounds for most of the doors that the player unlocks from within cyberspace. Since you never hear alert messages in cyberspace, these are all unused. In addition, the "locked" strings are unused since you cannot re-lock doors that you've opened from cyberspace.
Grove jettison enable stage one complete.
An unused jettison-related message.
Door locked - no maintenance necessary.
This is a spoken version of the message you receive when trying to open the maintenance access doors early in the game.
Charging station inactive.
This message appears right before the "relay functioning correctly" message in the string resource. It may have had something to do with the "damaged" recharge station at the corner of the maintenance level.
Reactor Overload Fuse Bypassed.
Reactor Overload Access Granted.
Reactor overload in progress. All security personnel to emergency checkpoints. Blast door to Security level is now open.
A few messages that would have been played when setting the reactor to "overload", which never happens, as the game refers to it as setting the entire station to self-destruct instead. The text versions are also unused.
Destruct Access cancelled by SHODAN.
Non-Emergency Access shutdown by SHODAN.
Two different versions of the "pod launch cancelled by SHODAN" message that correspond to different points in the "destroy the reactor and escape" sequence.
Charging interrupted and robots reactivated.
This message would have been used when you deactivate the charging station on the security level. Again, neither the sound nor the string are used; when you disable the charging process, the player is simply greeted with a room full of hostile robots.
Security computer override necessary.
This receptacle is for isolinear chipsets.
Aborting program. SHODAN security system back online.
These relate to the process of using the isolinear chipset to access the inner part of the bridge. The receptacle itself never specifically mentions its purpose in the game, and it's not possible to remove/deactivate the chipset once you've installed it.
WARNING: rapidly falling air pressure.
This would have been used during the last stage of the bridge separation. The "stage 3" alert mentions the beginning of atmospheric depressurization, making this message redundant.
Welcome to the throne of God.
This is a short message from SHODAN that likely would have played as you entered the central room of the bridge. However, after you first enter the level, SHODAN remains conspicuously silent for the rest of the game.

Version Differences

Demo

The playable demo version of System Shock was released in late September of 1994.

In order to keep a smaller file size, several graphics were removed from the starting level, resulting in some noticeable cosmetic differences. This included the "damaged" portions of the map, giving certain parts of the level a much cleaner appearance, particularly the ruined areas connecting Gamma and Beta.

The organic graphics (grass, plants) were also removed. As a result, the mini-grove in Gamma quadrant had been completely removed.

Non-essential enemy sprites were also removed. For example, the cyborg warrior guarding the computer room had been replaced with a less threatening Hopper.

Some minor item-related changes were made as well. For whatever reason, the display name of the magnum's heavy slug ammo was changed. This is a somewhat obscure change, since the magnum on the first level is relatively well hidden, and you don't get very much ammo for it anyway earlier on.

The fire extinguisher and unused warecasing items switched names, both names being slightly adjusted in the process. This resulted in fire extinguishers showing the somewhat ambiguous name of "equipment" when picked up.

CD-ROM Version

The original floppy disk release of the game contained a few things that were improved or reworked in the enhanced CD-ROM release, some more noticeably than others. Apart from the minor engine tweaks, higher resolution support, and voice acting, cutscenes were also upgraded and some minor tweaks were made to the levels.

The files START1.RES, DEATH.RES, and WIN1.RES contain the original versions of the intro, ending, and death cutscenes. They are in a different format than the CD-ROM version's cutscenes, being animated bitmaps (like the Trioptimum V-mail sequences) rather than actual video files. DEATH.RES contains the most noticeable changes: the initial shot of the hacker's body being pulled into the Cortex Reaver looks completely different; the rest is more or less the same visually, but with fewer frames. The entire animation contains only about a third as many frames as the "enhanced" version.

WIN1.RES is the same as the final ending, but the animation ends at the shot of the TetraCorp battle armor and is missing the final zooming-out shot with the "System Shock" logo at the end. START1.RES is almost identical to the final opening cutscene, but lacks the first two seconds or so of the door being blown open by Triop security. Both of these cutscenes also have lower framerates compared to the CD-ROM versions.

All three of the files are still referenced by name in the CD-ROM version's executable, and are still present on the disc, though they are no longer used in any way.

There were also changes made to certain levels...

Reactor
The camera immediately across from the elevator has been slightly repositioned. In the floppy version, it's slightly higher up and pointing downward at the corpse on the ground, while in the CD version it's close to the ground and angled upwards.
Medical
Near the beginning of the medical level, there is a room with two hospital beds and a Serv-Bot. The CD-ROM version added a small illuminated compartment near the ceiling with Mira Stackhouse's severed head inside.
Research Labs
The piece of paper with the "engineer's report" about the alpha quadrant circuit breakers was added in the CD-ROM version.
Flight Deck
The title of the "we have a serious emergency..." log was tweaked to fix the date stamp.
Executive
The log about Beta Grove being closed off was recorded by a different person in the CD version. It's possible that Looking Glass wanted this one to be voiced by someone else, and so they changed the speaker from one minor character to another.
Security
The detention cells near the end of the Security level are impossible to open in the floppy version, because they're under a cyberspace lock that can never be opened. In the CD version, a switch was added in cyberspace to unlock the cells.

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