Corrected entry: Once the countdown to release the poison has been stopped, The Shredder cuts the supports of the tower holding the poison container so that it will fall and release the poison by smashing open. The turtles attempt to support the tower, but in order to save April they fail and the tower falls anyway. Then the movie forgets that the poison exists. The act of the tower falling gets rolled into another action sequence and after it completely smashes to the ground, no poison. The turtles don't even mention it.
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