Fundamentally, the problem is that you need to get the energy somewhere. Currently, we get it indirectly from sunlight. In a world with no ability to obtain sunlight (as the justification of the Matrix goes), the second law means that barring geothermal (which doesn't require humans as a go-between), the total usable energy will decrease to zero.

It's like recycling. Can you ever expect to get better materials, or more materials than you started with without putting anything else in? (Including energy)