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The Ancient Autobots was the name given to the life force and accumulated wisdom of the previous bearers of the Autobot Matrix of Leadership. They would manifest themselves when the Matrix was abused, though this was not always the case.
Generation One animated continuity
After Dead End and Wildrider removed the Matrix from Rodimus Prime, they presented their find to Galvatron, who placed the Matrix in his cannon, believing the Autobot relic would give him great power. However, his cannon merely fired a puff of smoke. Furious at the Stunticons' possible dropping of the Matrix and thus damaging it, he attempted to shoot them as he usually did when angered. However, this time a bluish energy shot out, and the entire throne room was haunted by the Ancient Autobots (including Optimus Prime). The ghosts demanded Galvatron return it or they would haunt him all his life. Fearful, Galvatron quickly decided to remove it from his cannon, though he ordered it be disposed of rather than returned to the Autobots.
Strangely, when Scourge then took the Matrix, these Ancient Autobots did not manifest, although he did go mad with power in the process. It is possible that this is a way the Matrix or its inhabiting spirits punish abusers of their wisdom who are not already insane.