I would think that only the missing matter in galactic halos are hot, and the "fillaments" between galaxies cooler. According to the simulations its like a big cobweb, with galaxies forming at the intersections. 
Are you saying that the heat does not really exist?
What could be generating that much X-ray radiation to cause that much heat? A Blackhole?
That bottom picture looks just like an illustration of the synaptic connections in the brain.