Dark Matter is an entity born out of the negative feelings of all the Pokémon in the world. By absorbing a Pokémon's life energy, it has the ability to turn them to stone. When a Pokémon's body is turned to stone, its spirit is sent to the Voidlands, a dark realm swarming with Void Shadows, Dark Matter's minions capable of taking on the form of Pokémon. Dark Matter is also able to possess Pokémon that have even the smallest amount of darkness in their hearts. Using its mind-controlled slaves, Dark Matter turns Pokémon to stone to absorb their energy and grow stronger. Its ultimate goal is to "return the world to the void", namely to cause its spinning to stop and make it be consumed by the sun. It attempts to accomplish this by absorbing energy from the Tree of Life, the source of all the life in the world.

A long time ago in the past, when Dark Matter first surfaced, Pokémon fought against it to prevent their world from being destroyed. Alongside those Pokémon, a sole human also joined the fight. Due to the stars aligning just right in the sky, Dark Matter was finally defeated. However, the negative feelings that Dark Matter was made out of rained over the world, ensuring that Dark Matter would one day rise again. The ancient Pokémon, foreseeing this, prepared certain countermeasures for the future, such as sealing a spring of Luminous Water on the top of Revelation Mountain, holding the power to turn Pokémon back from being turned to stone. Mew, a Mythical Pokémon who had acted as a leading figure during the battle against Dark Matter, sent its spirit into the future to be reborn during the era in which Dark Matter would resurface.

During the events of Pokémon Super Mystery Dungeon, Dark Matter is first mentioned by ancient writings in the Voidlands, where the player, their partner, and most of the Expedition Society are sent after Nuzleaf, Yveltal, and Beheeyem possessed by Dark Matter turn them to stone after the player breaks the barrier over Luminous Water spring on Revelation Mountain. During their journey through the dark realm, they also learn bits of the past and come to understand bits of Dark Matter's history.

Later, after the Cobalt and their Mischief return to the real world, they rejoin with their remaining allies, and eventually make their way to the Tree of Life, which is withering and dying due to Dark Matter's influence. After defeating Dark Matter's minions, the group witnesses as the Dark Matter causes the Tree of Life to lift into the air and start flying away from the planet, meaning to pull both the tree and the planet into the sun. However, thanks to the combined efforts of multiple Pokémon, including Deoxys, Rayquaza, and Mewtwo, the tree's ascent is significantly slowed down, giving the Cobalt and their Mischief time to reach Dark Matter. After Arceus teleports the two to the Tree of Life, their Harmony Scarves cause them to evolve to their final stages for the third time, protecting them from the cold temperatures and thin air in the stratosphere. While climbing the tree, the duo encounters Nuzleaf, Yveltal, and Beheeyem, whom they free from Dark Matter's binds.

Ultimately the Cobalt and their Mischief confront Dark Matter at the top of the Tree of Life, where it traps them into a pocket dimension of its own making. Knowing that the tree isn't completely dead yet, the duo engages Dark Matter in battle. However, just when it seems like they have almost won, the Tree of Life finally runs out of energy, allowing Dark Matter to regenerate itself, assuming a new sphere form to protect its core, while the Cobalt and their Mischief are forced to revert to their original stages and all their current emeras are lost. Although Nuzleaf, Yveltal, and the Beheeyem try to attack their former controller, they all end up being turned to stone. Despite initial discouragement, the Cobalt and Mischief start fighting back, revitalizing the Tree of Life and engaging in yet another battle against the Dark Matter, breaking it down bit by bit. When its core is finally exposed, Dark Matter tells the duo how simply breaking him would cause him to be born again in the distant future. Surprisingly, the partner still is ready to break Dark Matter, accepting its negative feelings as a part of how the world works. The partner strikes Dark Matter's core one more time, causing it to burst into pieces, faintly thanking the partner for accepting it.

Afterwards, Xerneas, the incarnate form of the Tree of Life, reveals that Dark Matter has now completely disappeared, having turned to sparkling light that faded into nothingness. Close to the ending of the main game, Xerneas made the Mischief "remember" that, in their previous life, they used to be Mew, having fought the Dark Matter alongside the Mischief in the distant past. Due to their past attempt of defeating Dark Matter having actually failed, Mew and the Cobalt had agreed to have their memories erased by Mew, all in an attempt to avoid repeating their mistakes in the future. As the Mischief had accepted Dark Matter, it had disappeared for good, but doing this had also caused the part of Dark Matter that originated from Mew to disappear as well, forcing the Mischief to leave the Pokémon world after explaining the truth of their past to the Cobalt.

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