In episode 39, "Crisis," Optimus Prime held the Matrix of Leadership, but quickly put it away when the Autobots returned to their base. Jetfire and Optimus were about to leave for the Decepticon ship (to stop the Hydra Cannon from destroying the Earth), when Optimus insisted that Hotshot should take the Matrix in case anything should happen to him. Hot Shot refused and walked away. Jetfire and Optimus left with the Matrix. However, after Optimus died protecting the Earth, the only thing left was the Matrix found by Jetfire.
In episode 42, "Miracle," Optimus was resurrected by the power of the Matrix, and with help from the Minicons.
In the last episode, Megatron was defeated by Optimus. While drifting through space, Optimus encountered the Matrix. Seeing it, he said that he didn't 'deserve to wear it'.
Transformers: The Movie (1986)
In the original Transformers film, the Matrix was given to Ultra Magnus when Optimus Prime died on the examining table. It was almost dropped on the floor when Prime died, but when Hot Rod scooped it up, a blue glow surrounded him before giving it to Magnus. When Magnus, Blurr, Springer, Arcee, and Daniel crashed on the planet of Junk. they had to fight off the Junkions led by Wreck-gar and then tangled with Galvatron and his new minions. The Matrix was then stolen by Galvatron who wanted to use it to make Unicorn his slave. During the fight inside Unicron, Hot Rod wrestled the Matrix away from Galvatron and opened it to "light their darkest hour' meaning it was the only thing that could destroy the planet-eating robot.
Transformers: Revenge of the Fallen
In this film, the Matrix was hidden in Egypt by the 7 Primesx.
An alternate version of the Matrix is called the Dead Matrix and is controlled Nemesis Prime.