Sydney and Dixon were sent by Sloane to the plant to steal the Hensel Vaccine Inhalers and blow it up in order to prevent Hensel Corp. from selling the vaccine to a neo-nazi faction, although it was just a cover story. In reality, he wanted the vaccine for himself. Vaughn told Sydney that she needed to not only switch the inhalers with a fake copy, but prevent the destruction of the plant so CIA agents could sift through the plant's files.
Sydney infiltrates the lab and acquires the inhalers, rendezvousing with Logan and his partners on the staircase after disarming Dixon's detonators. She exchanged the inhalers with him and took a set of phony ones to Dixon, where both of them waited outside of a deserted plant. Dixon activated the bomb, but nothing happened, which meant they had to leave. However, Dixon had another charge with him, which he used to blow up the plant -- with Logan and his team still inside.