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The Malignant was a force that appeared during the Last Great Time War and neutralised the Cyclors. (COMIC: The One) River Song hypothesised that it was a higher-dimensional gestalt caught in quantum flux and mutuated constantly. (COMIC: Running to Stay Still)
The Cyclors were warped by Alice Obiefune's activation of the Psilent songbox. The energy of the Songbox also touched a Volatix Cabal Dalek mutant, who deformed them further, turning them into the Malignant. (COMIC: Fast Asleep)
During the Time War, the Malignant killed fifty generations of the Overcast. The Overcast blamed the War Doctor for this, accusing him of creating it. The Malignant was still present on the Overcast homeworld nine hundred years later, when the Eleventh Doctor was brought to the planet to pay from his "crimes". (COMIC: The Then and the Now)
By the time the Malignant caught up with the Doctor after his visit to Clundanius XI, it had become an infectious pathogen. The Malignant breached The Doctor's TARDIS and attacked River Song and infected her body. The Doctor placed her in stasis to prevent it from corrupting her personal timeline and removing her from history. (COMIC: Running to Stay Still)