Major Story Arcs
The Predacon known as the Shokaract was cornered by Maximal, he stumbled into a cave, where a dark whisper to him with promises of incredible power. Shokaract found the Dark Essence, the remnants of Unicron from after his defeat.
Shokaract created the Matrix of Conquest for housing the Dark Essence, assigned himself the name Shokaract and took command of a portion of the Predacon forces. With the Predacons support and the power of the Matrix of Conquest, Shokaract conquered Cybertron.
The Dark Essence weakness lied in the past and when Shokaract sensed temporal disruptions that threatened it and sent two Heralds. When both failed, Shokaract himself went to prehistoric Earth during the Beast Wars to defend the Dark Essence. Shokaract's presence warped reality, and Transformers from alternate universes appeared and gathered to attack. During this battle, Shokaract revealed the Matrix of Conquest and used its powers to destroy the attackers. The Covenant used this opportunity to combine their essences and enter the Matrix, severing the bond between the Matrix's Dark Essence and the Dark Essence of the past, thus allowing the Dark Essence to be drawn into overspace and avert Shokaract's timeline.
Out on a routine survey mission, the Predacon Shokaract found capsules containing an energy he was unfamiliar with, Angolmois. Upon trying to analyze it, the energy suddenly stirred and swiftly invaded his body, forcing him into a hibernation state. While in this state it reformatting his damaged body. To ensure continued control of the Angolmois, he forged a container for it, which he dubbed the Matrix of Chaos.
Shokaract kept the Matrix of Chaos housed inside his chest, fully integrated into his systems. He believed that using the energies of the Angolmois, and by plunging Cybertron into a bloody genocidal riot, the Anti-Matrix would "awaken" and facilitate his ascension as one of the "Masters of Misrule". Before the Anti-Matrix could awake, Magmatron had Shokaract sent to chronospace. There he was enlightened to what would happen if the Anti-Matrix would be awoken: rather than becoming a god, Shokaract would be consumed by the Angolmois and be sacrificed in order for Unicron to be reborn. Hearing this, Shokaract rippped the Anti-Matrix out of his chest, and as as a result killed himelf to prevent Unicron's rebirth.
When an Optimus Prime from an alternate universe was kidnapped by Unicron, he was corrupted and within him he carried the Matrix of Leadership. It was also corrupted and was made into the Decepticon Matrix of Conquest or the Dead Matrix.
Being the opposite of the Matrix of Leadership, instead of being harmful and fatal to Unicron it is instead harmful to Primus instead. Nemesis Prime tried to use it on Primus and nearly succeeded if it were not for the intervention of Omega Prime from an alternate Universe. Though Nemesis Prime was defeated and the Dead Matrix stored away, Soundwave of the Cybertron Universe had his servant Lazerbeak break in and steal the matrix. The duo then flew near the blackhole that was created from Unicron's demise in Energon and threw the dead matrix into the void causing Unicron to be reborn and continue his reign of terror through out the universe.