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In the IDW continuity, Darkwater is a covert paramilitary mercenary organization seemingly led by Colonel Wesley Knight, which was seen working alongside Agent John Bishop and the Earth Protection Force (EPF) for a period of time. At the behest of the EPF, they gathered extensive intelligence on the mutants of New York City—such as the Foot Clan's leadership and the Mutanimals—without the knowledge of those mutants.

They first came into open conflict with the Turtles at the T.C.R.I. building during the events of The War to Come, during which they attempted to capture the Turtles with a sonic cannon and tranquilizer darts. Bishop demanded all of Darkwater's reinforcements be brought in, and the building was soon invaded by squadrons of trained mercenaries.

Their service to the EPF ended during a standoff between Bishop and Old Hob, who had responded to the capture of the Mutanimals by kidnapping Wesley's wife Pam Knight and Bishop's father. Knight realized that he was in the wrong and ended all cooperation between Darkwater and Bishop, handing Bishop over to the Mutanimals' custody in the process.

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