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It comes down to Duke vs. Cobra Commander, and after taking another nasty beating like he got from the BAT, Duke actually talks CC into defusing the brainwave bomb - and killing Dr. Monev - by appealing to his ego, making CC realize he only wants Cobra to win if he's the one in charge of it.

CC makes a dramatic exit by casually stepping off the roof of the MARS building, and then shows up unharmed in his next scene, raising the question of how much of him is still human.

Now that this first arc has established the core cast of the Joe vs. Cobra conflict, the setup for the next arc seems to be exploring greater connections between the Joe side of the Energon Universe and the Transformers side. On the Joe side of things, we get the reveal of Hound that was unfortunately spoiled months in advance; on the Cobra side, CC finally lets Destro know about Megatron and reveals a spherical object that is apparently core to his plans, similar in appearance to the Matrix of Leadership's core.