For example what is the purpose of the universe? Is this the only universe? Is it a simulation? Is everything predetermined?
If it would be, we could scientifically test for the limits of the experimentation model. You can say, all of science is doing this effectivly. So far, no flaws have been found. If there were flaws, then within our models, so we adapt them, systematically approaching reality.
Now sure, if there would be an allmighty god, we would have no chance proofing him or her, that is tautological. But if it would be "just" aliens of a higher level, doing rat lab experiments with our universe, we could figure that out eventually.