This encyclopaedia contains lots of spoilers - you should play through the campaigns first before reading too much here!
NEXUS Intruder Program
Overview
In Campaign 3, NEXUS summarises the purpose of the Intruder Program:
Such an interesting history lesson. Now allow me to bring you up to date. The NEXUS Intruder Program was created to control fools like you. It's very simple for me to infiltrate your systems and take them over. It's so simple in fact that you wouldn't even know that I was there. That is until I have to activate parts of myself etched in to your core systems. Let's start by activating NEXUS in your core system and see what happens! Whahhh-hah hah!
However, this is a somewhat benign description of the Intruder Program, compared to this briefing from Project HQ during in Campaign 1:
We are not sure what NEXUS is, or who or what is directing it. Initial research links the NEXUS Intruder Program with The Reed Corporation, the developer of the Synaptic Link. We have ascertained that NEXUS supplied the New Paradigm with most of it's technology. Whatever Nexus is, it's more than a computer parasite. It has technology... and weapons. It knows about us and it is not friendly.
The important distinction to make is that the Intruder Program is not NEXUS. The Intruder Program is a technology under the control of NEXUS. It's used to infiltrate computer systems so that NEXUS can take control of them. It's what NEXUS then does with those systems that makes the Intruder Program such a significant threat.
What is it used for?
After gaining control of a computer system via the Intruder Program, NEXUS finds all sorts of ways to cause you pain and suffering:
- Disruption of communications
- Spying on your plans and technologies
- Causing your technologies to fail
- Assimilating your technologies and using them to fight against you
How does it work?
The Intruder Program is a self-mutating computer parasite that targets core computer systems and then reprograms them from within.
For the Intruder Program to gain access, NEXUS must first find some way to connect to that system. In the early stages of the game, this is achieved by various communication links, such as Satellite Uplink stations. Later, a special "Nexus Link" turret is created that can use an electromagnetic beam to gain access to nearby computer systems and infect them.
Once the Intruder Program gains access, it first isolates itself from other parts of the system, making it very difficult to detect or eradicate. As it slowly takes over more of the system, it will attempt to spread to other systems as if it were a computer virus. If it is detected, it will destroy it's memory banks and remove all traces of external communications to prevent researchers from determining its goals or finding out where it's being controlled form.
Once infected, systems can be controlled by NEXUS - the virtual cybernetic consciousness of Dr. Alan Reed.
See sub17fmv transcript for more detailed information and screenshots.
How was it developed?
After patenting his Synaptic Link technology in 2080, Dr. Alan Reed became the lead scientist responsible for Cybernetics research at NASDA in 2085.
Unknown to NASDA, Dr. Reed was using most of the money to secretly fund research of the Intruder Program at facilities owned by The Reed Corporation.
In 2088 the military cancelled Dr. Reed's cybernetics research programme citing lack of progress - hardly surprising considering he was secretly researching NEXUS instead!
Without money from the cybernetics project, The Reed Corporation went bankrupt leaving Dr. Reed unable to continue his NEXUS research. Dr. Reed was furious and vowed revenge on all who stood in the way of completion of the Intruder Program.
It is not clear exactly when Dr. Reed completed the NEXUS research, however it must surely be after 2088.
 This poses a serious timeline issue as The Collapse, caused by NEXUS, was supposed to happen in 2085. See: forum discussion for more info.
The face of NEXUS
When communicating via the Intruder Program, NEXUS appears as a 3D wireframe face rather than the NEXUS logo. The similarities between the Intruder Program face and Dr. Reed's face are striking:
  Â
This leaves little doubt that Dr. Reed did in fact complete his NEXUS project and upload his consciousness to it. Furthermore, it then becomes clear that it was Dr. Reed who used the Intruder Program to infiltrate NASDA computers and take revenge on "all those who stood in his way" by causing the system malfunction that led to The Collapse.
The colour of the face will change depending on Dr. Reed's state of consciousness. When he's feeling indifferent to the situation his face is generally green, but if he's feeling angered or agitated the face will appear red, often with a purple glow. Sometimes, his eyes will glow indicating that he's focussing his attention and determined actions on you. There are also many scenes where a yellow voice waveform will appear under the face. Often a circular disc will appear behind the face, indicative of the logo used for The Reed Corporation.
Technologies
The following technologies are related to the Intruder Program:
- Nexus LinkÂ
- Nexus Resistance Circuits
Trivia
Nexus' forehead has the word "REEDBROW" (as in Dr. Reed's Brow) written on it. Nexus' lower lip has what appears to be the word "KENTUCKY" (as in Kentucky Fried Chicken?) written on it. Furthermore, the number "666" appears above Nexus' right eye. These were discovered on a digitally remastered version of Deliverance.
Media
See tag "nexus" for a list of audio, video and articles relating to NEXUS and the Intruder Program.
References
 The following videos provide key background information in to the Intruder Program:
- cam1out5 transcript – Several pertinent observations from Project HQ about Nexus
- cam3abf transcript – Explains the research and timeline associated with the Intruder Program.
- sub17fmv transcript – Explains how the Intruder Program works.
See also
- Dr. Alan Reed – creator of the Intruder Program
- NEXUS – post-Collapse faction
- The Reed Corporation – Company that did initial research on NEXUS