Retrieving the CABAL core pieces
Following Nod's close defeat at the end of the Second Tiberium War, the power struggles that had ended upon the return of Kane once again began to unfold. Anton Slavik attempted to lead Nod according to Kane's plan, however, the Inner Circle, led by Marzaq, began to carve up Nod once again. Without CABAL, Slavik realized that he lacked the logistical infrastructure needed to effectively hold Nod together, and ended up ordering the commander to assassinate Slavik's rivals. Following a heated meeting with the Inner Circle, he gave the commander the task of reclaiming CABAL from the ruins of the Cairo Temple of Nod. Using a small scout team, he managed to succeed in regaining the three segments of CABAL's mainframe.
Following the orders of CABAL
Once reactivated, Slavik allowed CABAL to issue orders to the commander. First, the Commander was sent to the Genesis Pit, and ordered to let loose the fierce tiberian wildlife that lived there. Then, CABAL ordered the assassination of Tratos and several attacks on the Forgotten, to destabilize the trust between GDI and the mutants. The commander carried this out faithfully, supposedly "in the name of Kane".
However, it became clear that CABAL had been acting alone in these ventures; when the Inner Circle tried to reign him in, he rebelled, killing all but Slavik, who escaped. The Commander's troops barely made it to the Montauk before the now renegade cyborgs caught them. Slavik then proceeded to order the capture of a GDI EVA, in order to replace CABAL in its logistical capacity. With this, a strike was launched on what was believed to be the CABAL Core, however, this turned out to be a decoy.
The final stages
However, Slavik made the one move that CABAL would never have suspected him to make; he made a deal with Paul Cortez, the General in charge of GDI's Firestorm Taskforce. Putting aside their enmity, the two agreed to share intelligence, then planned a joint assault against CABAL's true core.
The Nod Commander attacked CABAL's harvesting operations while protecting nearby civilians. Destroying this, his army participated in a joint assault on the Core, helping GDI deactivate the Firestorm barrier protecting it.
His current status and whereabouts are unknown, though as a Slavik loyalist, he may have been targeted by Marcion.