Medial septum (MS) is important for theta generation by either a unitary pacemaker timing signal imposed on the hippocampal system or assisting in organizing target subcircuits within the phase space of theta oscillations. Therefore, this study used temperature manipulation of the MS to test these models. Long Evens rats were water restricted for 22 hours and trained to perform the behavioral task prior to surgery. After recovery from surgery, the animals were water restricted again to perform a spatial alternation task in a theta maze. The behavior session lasted 40 minutes and then cooling was applied by manually placing a small amount of dry ice in the cooling chamber. The dataset includes behavioral and electrophysiology data. The data indicate that septum is critical for sustaining precise theta phase coordination of cell assemblies in the hippocampal system.