Hybrid nanofluids have caught the attention of scholars and investigators in the present technological period due to their improved thermophysical features and the desire to boost heat transfer rates compared to those of conventional fluids. The present paper is mainly concerned with heat transmission in cone-disk geometry in the presence of a magnetic field, activation energy, and non-uniform heat absorption/generation. In this work, the cone-disk (CD) apparatus is considered to have a rotating cone (RC) and a stretching disk, along with iron oxide and cobalt ferrite-based hybrid nanofluid. Appropriate similarity transformations are employed to change the physically modeled equations into ordinary differential equations (ODEs). Heat transfer rates at both surfaces are estimated by implementing a modified energy equation with non-uniform heat absorption/generation. The outcomes illustrated that the inclusion of such physical streamwise heat conduction variables in the energy equation has a significant impact on the well-known conclusions of heat transfer rates. To understand flow profile behavior, we have resorted to the RKF-45 method and the shooting method, which are illustrated using graphs. The findings provide conclusive evidence that wall stretching alters the flow, heat, and mass profile characteristics within the conical gap. The wall deformation caused by disk stretching was found to have a potential impact of modifying the centripetal/centrifugal flow characteristics of the disk, increasing the flow velocity and swirling angles. A rise in activation energy leads to an improved concentration field.