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Either you already have it or yes, you missed it.

Upon entering Team Aqua's hideout, take the top right Teleporter, go down the strairs at the top left where a grunt is guarding, continue going left, step on the teleporter, in this room there is a scientist staring at the monitor, walk towards him and take the Teleporter on the right, straight to the next teleporter to the left and enter this room and there you have it, Dark Pulse

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