As Starscream and Soundwave found Skyquake in his stasis chamber on Earth, the energon cube was used to revive the Seeker from his centuries-long stasis. In One Shall Rise, Part 1, Megatron had his Vehicon troopers harvest some Dark Energon and place them in cubes. In Orion Pax, Part 1, Starscream attempted to steal a bunch of energon cubes for himself but dropped them when he encountered Optimus Prime. In Armada, Bulkhead found a stash of energon cubes in a ditch that were ready for transport to the Nemesis and found himself piled in the cubes after falling in the ditch. He was transported with the cubes onto the Nemesis. In Flying Mind, Megatron had placed a cube with Dark Energon, which had given the ship a sentient mind. It was stopped when Jack Darby was able to get the Dark Energon cube out of its core.
Two piles of Energon cubes were seen in an episode of Transformers: Robots in Disguise called Can You Dig It? Ped stole a bunch of the cubes from the Autobots for himself and planned to steal all of the cubes on Earth so that he could monopolize enough to so he could negotiate with other Decepticons. However, his plans were foiled by the Autobots and he was placed in a stasis pod.