Council of Clones is the 27th episode of The New Adventures of He-Man.
Skeletor has been frequently bombarding one area of the shield of Primus, forcing the Inner Councilors to concentrate all of their energy on that sector, and Mara says that he and the councilors desperately need rest. Master Sebrian is also tired from the recent attacks. Without the full power of the shield, the Evil Mutants will surely penetrate it.
On the Mothership, Skeletor, Flogg and Slush Head, watch on as they bombard the shield with everything they got. Flogg is surprised, when he learns that Skeletor wants Primus to attack them, so he can unleash his newest invention, the Super Computer. As Primus fights back with Starship Eternia and Astrosubs, Skeletor releases a small shuttle from the mothership containing a super computer, which He-Man captures. He-Man heads off to attack the Mutants and stop the attack and takes the shuttle back to Primus, with Master Sebrian's consent.
He-Man feels weary about bringing the Super Computer could be dangerous, but brings it to the Scientists anyway. Gepple, Alcon, Krex and Meldoc discover that the super computer contains the ability to produce Clones, and they decide to produce clones of the Inner Councilors, so that the real councilors can finally have some rest. The Scientists build a chamber in which they plan to use to clone the Inner Councilmen. Skeletor learns of their plan and activates the machine, which causes the clones march out and aggressively dispose of the Scientists in a chamber. As Master Sebrian explains the plan to the real Inner Councilmen, the clones march in and take their place.
Soon after, Sagitar tells Sebrian that the shield is down and Skeletor is on his way with the Mutant Armada. Werban tells He-Man that the Clones have put up a shield around the Council Chambers. The shield is so strong that it shorts out the energy of the Sword of Power. Sagitar and Spinwit fly out to confront them, fully loaded with Hologram Projectors, to fool the Mutants that they are being attacked by an armada of Astrosubs.
Meanwhile, He-Man journeys to the Scientists' Laboratory to destroy the Cloning Super Computer. When he arrives at the lab, He-Man frees the Scientists. The Scientists discover that their technology cannot destroy the computer. Meanwhile, Werban blames Master Sebrian for this disaster. Sebrian purposes that they all focus their mental energy on the shield, hoping that they can weaken it.
Skeletor and Flogg become concerned that the Astrosubs are multiplying. When the Mutants realize that the Astrosubs were illusions, Skeletor boards a Shuttle Pod and heads towards Primus. Caz spots Skeletor's Shuttle Pod and runs to tell He-Man.
As He-Man uses all his strength to destroy the Cloning Super Computer, Master Sebrian manages to get through the shield around the Council Chamber. As Sebrian goes through the shield, a weakened He-Man is attacked from behind by Skeletor and Slush Head. Master Sebrian confronts the Clones, who weaken him with their magic. The Sorceress telepathically contacts Sebrian, to tell him to use his staff to draw the Clones' power. With that, He-Man's power returns and he defeats Skeletor.
With the shield around the Cloning Super Computer weakened, He-Man uses the Sword Of Power to destroy it. As the Clones disappear, Skeletor and Slush Head disappear in a puff of smoke. Once the real Inner Councilmen use their power to return the shield, Flogg becomes frightened and calls for a retreat.