The Microwave Emitter was an experimental weapon developed by Wayne Enterprises in Batman Begins. The weapon was designed to be used to vaporize large amounts of water using focused microwaves. It was stolen and used as part of Ra's al Ghul and the League of Shadows plan to vaporize the water supply of Gotham City that had been contaminated with Scarecrow's fear toxin to induce the population into a state of panic to destroy the entire city. It was transported around the city in a SWAT vehicle and then moved to the Gotham Monorail train until the plan was foiled by Batman.
The microwave emitter was a prototype weapon developed by Wayne Enterprises designed to be used in desert warfare to vaporize the enemy's water supply by using focused microwaves. Lucius Fox said that it was rumored that the emitter was tested in the dispersal of chemical agents into the air by vaporizing water and he believed that doing that was illegal.
While the prototype was being transported on a freighter to Gotham City, two henchmen of the League of Shadows activated it and killed the rest of the crew. It was then brought on-board another ship, which was investigated by Carl Finch and then killed when he discovered it. When it went missing, Lucius was fired from Wayne Enterprises by CEO William Earle for asking too many questions about it.
When the time came for the League to destroy Gotham, the emitter was transported along with Ra's al Ghul around Gotham in a SWAT vehicle. It was then mounted onto the Gotham Monorail System. As the train headed towards Wayne Tower (where the main water hub was located), the emitter vaporized water in the mains and thus released the fear toxin. By going into Wayne Tower, the emitter would have vaporized all of the city's water and thus the entire city would have been covered in fear toxin. Batman, with help from James Gordon in the Tumbler, was able to stop the train from reaching Wayne Tower. As the train fell into a parking garage, the heavily-damaged emitter exploded and killed Ra's al Ghul.