How do thoughts work at the neuron level? How does thought work at the biological level of individual neurons? I believe there are many neurons which are active in the brain at the same time. For example, our senses are constantly taking in sensory information on a continual basis. However, most of the neurons activated by sensory input are not capturing our attention, and as a result, our thoughts are elsewhere. I believe that thought, an "active cognitive process," is a collection of neurons which are responsible for engaging our complete attention. This collection of neurons shifts as our attention shifts. But this does not explain what is responsible for controlling our attention at the neural level. Can't find any answers to this question.
It has been proposed that spontaneous cortical activity may have a lot to do with cortical processing not related to external sensory.  


  Within a spontaneously active network, we observe the sudden “ignition” of one out of many possible coherent states of high-level activity amidst cortical neurons with long-distance projections. During such an ignited state, spontaneous activity can block external sensory processing. We relate those properties to experimental observations on the neural bases of endogenous states of consciousness, and particularly the blocking of access to consciousness that occurs in the psychophysical phenomenon of “inattentional blindness,” in which normal subjects intensely engaged in mental activity fail to notice salient but irrelevant sensory stimuli.


The spontaneous cortical activity itself has been studied at a more reductionist level where they've been separated into multimodal functional motifs.  Perhaps these functional motifs form the basis for the nature of stray thoughts.