Agatha Heterodyne, the engines and were "...used to electrically saturate the air around Mechanicsburg..." allowing the hand-held lightning staff to of raw electricity. Another poor soul noted that the air sparking another theory. While the slick feel could be due to the ionization of the molecules in the atmosphere, it has been proposed that it actually due to the release of that will carry the lightning from the staff to its intended target. Either way, for the power to take down the clanks, multiple engines were needed and at least six of who-knows-how-many ended up sacrificed for Mechanicsburg's protection. Perhaps Gen2 of these will be able to hold up better — at last beyond two discharges, if such future opportunities should arise.
Evidence and logic show that all great Spark weapons require a power source. For Gilgamesh Wulfenbach's lightning staff to destroy invading war stompers, the atmospheric ionization engines are that source.
The inspirational source material for the whole system seems to be related to the principles of the electric foils based on Gil's while on board the Castle Wulfenbach. This does not exclude the possibility that the lightning moat may have similar technological ancestry as well. If it was, in fact, the foils, then these engines would be related to the Heterodyne device. Visually, the engines seem to be a cross between that device and a certain clank's head.
They became a plot point again when agatha used them to generate a massive enough lightning strike to rechage the castle. done with a modification to the control rod. the engines had been repaired by the mechanics burg people.