The Dark Spark is a dark relic that was said to be the equal but opposite force to the Matrix of Leadership. Whilst the Matrix granted wisdom, its antithesis allowed its user to bend the fabric of the universe and its inhabitants to its will. Possessing some connection or similarity to Dark Energon, it can reanimate the dead, granting it's owner command of them. It also apparently has the ability to travel between universes, as well as possible time travel. The Dark Spark is not to be confused with the Decepticon Matrix.
The Dark Spark's creation was debated by ancient Transformers such as the Patterners and the Disciples of the Thirteen. One group claimed that it was the Spark of Unicron himself while the other saw it as the ejected corruption from the Well of All Sparks. After witnessing its dark power, the Crystal Guardians from Crystal City decided that this artifact needed to remain hidden forever and thus placed it within an underground vault protected by some of their warriors. In the aftermath, the Dark Spark was considered a myth.
In the Great War, Megatron came to believe in its existence and dispatched Shockwave, Soundwave, and Starscream to find it. This led these Decepticons into the underground levels of Cybertron, where they fought Insecticons and the Guardians before arriving at the vault containing the relic. After they disabled the security system, they found that Sideswipe and Ironhide had been following them. The two Autobots trapped the Decepticons in the vault and fought their way through a horde of Insecticons to bring Optimus Prime the relic at an old train station. Despite Starscream's attempt to stop them, they departed for Iacon on a train, only for Soundwave to detonate a bomb he had hidden on the track. Optimus tried to fool the Decepticons into thinking that he had the Dark Spark but Sharpshot saw through the ruse and deduced Ironhide was carrying it. After Sharpshot defeated Ironhide, Shockwave seized the relic and proceeded to Kaon with it, receiving back-up in the form of the Combaticons. At the gates of Kaon, Shockwave managed to enter with the Dark Spark by having Bruticus take Cliffjumper prisoner.
The Dark Spark was then given to Megatron, who inserted it into his chest. Shockwave designed an experiment, with Cliffjumper as one of the test subjects, that would use the Dark Spark to remove an Autobot's will to fight. Cliffjumper escaped with the help of Optimus and Jazz before this could bear fruit and Optimus Prime came to the lab where Shockwave and Megatron were. Megatron displayed that the Dark Spark had some connection to Dark Energon and was able to use it to resurrect dead Autobots. Despite Megatron using Autobot Terrorcons as an army against Prime, Optimus bested Megatron in combat. Enraged, Megatron swore to rip the Matrix from Prime, who responded by unleashing its power on the Decepticon leader. Megatron tried to counter with the Dark Spark only to beaten again and knocked unconscious. The Dark Spark was blasted into another universe.
In this new universe, the Dark Spark was glimpsed by Lockdown, who was able to retrieve from the impact site despite resistance from Optimus Prime. Prime explained to Drift and Bumblebee exactly what the Dark Spark was, knowing of it through the Matrix. Lockdown schemed to use the Dark Spark's abilities to return to the height of the war on Cybertron, then bring the war into the present day, so that he would receive a continual flow of pay from Megatron. He was eventually confronted by Prime, who fought him, allowing Drift to remove the Dark Spark from the bounty hunter's chest. Prime used the Matrix to send the Dark Spark through time and space.
Arriving in yet another universe, the Dark Spark appeared as a purple comet, which was witnessed by Optimus Prime who had hoped the day would never come when he would have to face it.