Im interested in your explanation of the people involved in the attacks that occured on Sept 11, 2001. 
Also can you give an example of 'dormant' computer codes?
Let me jump on that last part.
Boeing and the Air Force have extensive configuration management tools and procedures. When I worked on AWACS software, one of my main positions was Configuration Management -- Software Integration and Testing. We performed audits that counted every single byte in every program installed on the mission computers. The audit compared those counts plus checksums to see what in the software was changed. When a programmer submitted documentation for their code changes, it included the number of bytes increase or decrease (or zero) for every software package, We also did a line by line comparison of the hexadecimal dump for every line of code.
If anything was changed and not documented, or if the comparisons showed something unexpected, we'd deep dive into the source code to see whether the code or the documentation was wrong. Usually it was the programmer's error by submitting source code they tested. Sometimes to fit larger code into existing system software to test, they had to remove unnecessary sections, and sometimes they forgot to replace what they removed. Other times, they didn't compile the code properly, so we provided the most current libraries and operational code to use for their tests.
Configuration Management (CM) performs a very important function. Most people don't realize that the bulk of mission software (including for AF1) is stored on magnetic media, The compiled software is loaded onto the computer/s before every mission. Because of this, it's impossible for any "covert surveillance bug code" to exist. Once the aircraft lands, the crew does a wipe of all the data so the next sortie will again have a fresh installation of the latest tested software.
Even systems like secure comms have their firmware removed and replaced frequently.
So, I find it highly unlikely that anything that could snoop on AF1 communications or data would exist beyond the initial reloading of the operating system and databases.
The software I maintained was classified SECRET. if we left the software loaded while the plane was parked for extended periods, the chances of corruption or compromise becomes higher. Wiping the storage and rewriting the memory many times over is the only way to make sure the mission systems can't be monkeyed with or stolen.
In layman's terms, every time you leave work for the night, you back up your data files to a server, then do a complete disk wipe on your PC. Each morning, you would reinstall the operating system and applications from an image of a working PC. If the PC is stolen, a new replacement is easy to load and have running 100% in a few minutes by restoring the O/S image.
I hate when people assume they know everything when they have zero experience working with actual computer systems like the one in question.