Intermittent fluid flow has recently been identified as an important transport mode for processes involving subsurface multiphase fluids such as CO2 storage and natural gas production. However, due to experimental limitations, it has not been possible to identify why intermittency occurs at subsurface conditions and what the implications are for upscaled flow properties such as relative permeability. We address these questions with observations of nitrogen and brine flowing at steady-state through a carbonate rock. We overcome previous imaging limitations with high-speed (1s resolution), synchrotron-based X-ray micro-computed tomography combined with pressure measurements recorded while controlling fluid flux. We observe that intermittent fluid transport allows the non-wetting phase to flow through a more ramified network of pores, which would not be possible with connected pathway flow alone for the same flow rate. The volume of fluid intermittently fluctuating increases with capillary number, with the corresponding expansion of the flow network minimising the role of inertial forces in controlling flow even as the flow rate increases. Intermittent pathway flow sits energetically between laminar and turbulent through connected pathways. While a more ramified flow network favours lowered relative permeability, intermittency is more dissipative than laminar flow through connected pathways, and the relative permeability remains unchanged for low capillary numbers where the pore geometry controls the location of intermittency. However, as the capillary number increases further, the role of pore structure in controlling intermittency decreases which corresponds to an increase in relative permeability. These observations can serve as the basis of a model for the causal links between intermittent fluid flow, fluid distribution throughout the pore space, and the upscaled manifestation in relative permeability.