Welcome to the fight jadedamion.
The "Nuclear Effect", destroying most ships in a system and making it so that system can never again have supply with all itssresource nodes are destroyed, can happen a few ways.
Note that this is actually a pretty rare condition, most games will not see the "Nuclear Effect" happen.
The most common is either the player using a Nuclear Warhead or a Mining Golem destroying a system.
As noted, the Nuclear Eye will also do this if you trigger one of those.
The re-vamped Astrotrains have a "Nuclear" train that could do it, but the Astrotrains minor faction has to be set pretty high to see that.
The "Nuclear Command" option under the AI Plots page during game setup will also do this, whenever a Command Station belonging to the AI with this option enable dies, it will nuke that system.
There is also a semi-nuke effect that the Scorched Earth AI type uses. When a command station belonging to a Scorched Earth AI dies, it 'Scorches' that system making it permanently out of supply and destroying the resource nodes in the same manner as a nuke. However, it does not destroy most ships in the system like a Nuclear Explosion does when triggered.
It is probably not the case based on what Faulty Logic saw in your save, but a very few structures, such as the Co-Processor, block player supply in the system while they are still alive.
As for a help section, there is a wiki being put together (see my sig), but it's only about 60% complete at the moment.
Hope that helps and hope to see you around some more.
D.
