The website downtime lasted for an unusually long time this occasion, however, the experience I gained from fixing it nearly guarantees a 99% uptime from now on.
While upgrading Ubuntu on our Communications Server after moving all the dedicated game servers over to our new PowerEdge system, the communication server turned off after finishing the upgrade, and could not turn back on. Complaining of bad installation and missing packages, it was a problem I faced before with my laptop.
Be warned, users of Ubuntu 12.04 LTS! Do not upgrade using the built-in upgrade tool. Upgrading from 12.04 to 13.10 has, without fail, always left my machines utterly unusable. However, now that all of our machines are using 14.04 LTS "Trusty Tahr" we are unlikely to see the problem arise again.
The real problem became known after I had rescued the data from the Comm. Server and had it on a backup drive. I had copied raw data from our database without exporting it. Without having exported it, I was stumped for a notable period of time attempting to solve this puzzle.
Although of course now, at the end of all this, I find it somewhat pitiful that the fix was simply copying that raw data back into the database as root, and giving permissions back to the MySQL user.
Please make note of my learning experience, for if it happens again, I am the only one left to blame. If you blame anyone, blame me for failing to learn quickly enough.
All servers are now located on the PowerEdge.