Hi. Taking a look at this as this has been here the longest with no critique. Bear in mind I'm new to critting so if anyone else with more experience contradicts me, listen to 'em :P
Broad view: Unless I'm missing something and there is more than is being hinted at, I'm not entirely sure what SCP-4000 is other than a project that manipulated nuclear weapons testing. There's a bunch of stuff about the risk of subvertion by aliens but I'm not sure why that's relevant or worthy of so much space.
Likewise your first footnote describes something that anybody reading the document (if they were actually Foundation staff) would know already. I don't think you need any explanation of causality at all, never mind an in depth "Causality 101."
There are a few grammar errors, for example "to prevent a "Extratemporal Reconstruction Event"" should be an, "If a SCP-4000 failure" should be "If an SCP-4000 failure"
Some sentences are very long and unwieldly - like this:
In theory SCP-4000 can be subverted via an extraterrestrial entity but as far as the Foundation has been able to discern no entities from Earth3 can warp reality on an extra planetary scale meaning that SCP-4000 is only vulnerable to reality warpers above Class-V and [DATA EXPUNGED]
That's a big sentence right there, and it doesn't flow too well. Maybe…
"SCP-4000 could be subverted via an extraterrestrial entity. The Foundation is unaware of any terrestrial entities able to warp reality on an extra planetary scale. SCP-4000 is only vulnerable to reality warpers above Class-V and [DATA EXPUNGED]"
Not sure why that expungement is there. Why would that be expunged?
The original SCP-4000 operations have been covered under the guise of nuclear testing.
That's a bit unwieldly and probably should be in the description instead, or removed altogether.
The whole "SCP-4000-1 was a computer created by Foundation staff.." paragraph lost me a bit, as I don't understand why a computer that generates random numbers would have an SCP sub-designation. Too much details and not enough engagement.
…altered them based on SCP-4000-1's readings until the entire surface of the Earth was in some way causally linked1 to the radiation.
Once again, not sure what the significance of this is.
Overall (and once again I might be missing something here) there isn't enough here to engage the reader. I think rather than go into the minutiae of Class D's pushing buttons, you need to explain in greater detail what exactly the thing is doing, and then bring it back for crit.