I pose an alternate system of physics at the tiny scale. The goal is to refine it so that large particle accelerators are fraudulent devices as part of a government conspiracy, but as an earlier version of this question described it, the changes were too encompassing and required a conspiracy involving basically everyone.
So let's stick to the vaguest details for now. At some level, perhaps the quark level, what we think to be 3-dimensional is actually 4-dimensional (4 space and 1 time). We have different particles, and their different properties are related to how much they stretch into the 4th spatial dimension, and what is going on there. The 4th dimension accounts for what we thought was quantum irregularities and the gravitational influence of Dark Matter; this is my Fixion.
Governments are aware of the 4th dimension, and they have reason to believe it is filled with resources and possibly lifeforms. So the large hardon colliders are actually experiments to gather enough force in one place to overcome the gravity-like force keeping all observable matter confined to 3D space, and explore what lies off in the direction we cannot see.
For this setting, I am relying heavily on the fact that particles on the atomic scale and below are almost never directly observed, and that all of our models of chemistry, electromagnetism, etc., are just models that explain why different substances behave some way under certain circumstances.
My original idea was to make atoms themselves pure fiction, but that breaks too much of physics and resets our understanding to the 19th century. I am now considering quarks, or rather the sub-atomic scale, as the limit: anything smaller than an atom is false. Every paper ever written on quantum mechanics was either deliberate fiction or unwittingly based on fictitious models and assumptions. The government tells everyone to believe in quarks and bosons, and "invents" devices that "detect" such entities, like the Higgs particle, to further the conspiracy.
Assuming everything on the sub-atomic scale is a fraud and there is actually a 4th spatial dimension, who needs to be in on the conspiracy? Which of our models would have to be not just horribly misguided but deliberately made up, in order to allow for this dimension? The question is not whether a conspiracy can be maintained or not, the question is only to serve which branches of science and which technological devices I need to make deliberately fictitious. Everything else can just continue operating on working models that happen not to match the underlying reality.