After Etemon was defeated, he stayed inside the vortex he had been trapped in, refusing to return until he was powerful enough to defeat his enemies. He finally digivolved into the Mega-level MetalEtemon. He returned on a meteorite (most likely the burnt-out Dark Network core). Tracking down the Digidestined, he found Mimi, Joe, Palmon, and Gomamon, who were losing a battle to Puppetmon. Puppetmon and MetalEtemon got in a fight, and the two Digidestined and their Digimon used the distraction to get away. After a while Puppetmon got bored with MetalEtemon and left.
Later, MetalEtemon found the the same Digidestined again, now accompanied by Ogremon and SaberLeomon. During the battle, MetalEtemon summoned a blast of darkness from the sky that fatally wounded SaberLeomon. Zudomon managed to finish MetalEtemon off.