The Matrix was held by Prima, but eventually wound up with Primus in the Core. The Matrix became an object of legend among Cyberton. Several had dreams of reclaiming it and becoming the Prime that would lead Cybertron to a new Golden Age. When the High Council named Orion Pax the new Prime and gave him the task of finding the Matrix for himself, Megatron was enraged and vowed to find it for his personal use first.
When Primus was reaching to a critical state, Orion Pax went to Cybertron's core and tried to help Primus. Sensing potential and nobility within Orion, Primus gave him the Matrix, thus turning Orion Pax into Optimus Prime. The Matrix would subsequently guide and aid him through a number of adventures, including continued battles with Megatron and the Decepticons and conflicts with new foes such as the Star Seekers and the Quintessons. During the clash with the latter, Optimus would be forced to contend with the Quintessons' use of a Matrix Replica.
In One Shall Rise, Part 3, Megatron and Optimus Prime ventured to Unicrons spark in order to release the Matrix's energy directly into the chaos bringers spark. Although they succeeded, the energy that made Orian Pax into Optimus was gone and hence Optimus was once again his former self. Megatron took advantage of this and tricked his old friend into working with the deceptions.
Jack ventured to Cybertron with Arcee to refill the matrix using Vector Sigma. Using its key as a storage medium, they downloaded the collective wisdom of the Primes as well as all of Optimus' memories. When they returned to Earth, Orion was defying Megatron and about to be executed but Arcee held him off long enough for Jack to refill the Matrix and bring back Optimus Prime.
After the destruction of the old base, Optimus was severly damaged under the rubble. Smokescreen was able to rescue Optimus and shelter him in an underground cavern. There, they layed low and Smokescreen tried to comfort Optimus. After Smokescreen retrieved the Forge from the Decepticons, Optimus told him to use the hammer to restore Cybertron. Smokescreen insisted that he use it to restore Optimus, but Optimus said that the fate of their kind was more vital than saving Optimus's life. Optimus told Smokescreen that the time for a new leader was upon them and that Smokescreen was Optimus's choice. This left Smokescreen puzzled for a few moments and Optimus was close to dying. The Matrix opened up and Smokescreen quickly used the Forge to restore Optimus in a new body.
After defeating Unicron, Optimus told his team that they have acted as a Prime, with or without the Matrix. As the team sadly watched Optimus fly into the Core, sparks flew out of the Well. One red spark, possibly Optimus' spark, shines out.
- Optimus only qualifies as a Prime due to possesing the Matrix of Leadership. Though Optimus has proven to be worthy of the Matrix. In the ending of Predacons Rising, Optimus told his team that they were worthy Primes, with or without the Matrix.
- The Matrix could turn any Cybertronian into a Prime. However, Optimus says the Matrix chooses the individual, only Optimus and Smokescreen have been judged worthy by the Matrix.
- The Matrix being used to hold the AllSpark is a reference to the Animated finale where the Animated Optimus Prime forged a Matrix-like container to hold the AllSpark.
- It is also possible that the Matrix can revive a Cybertronian's spark if it's placed in their chests.
- The first season of Transformers: Robots in Disguise gave no indication as to whether the revived Optimus still possesses the Matrix of Leadership.