The lightning gun fires, essentially, a basic laser rifle's laser. At the point of impact it generates a natural gas cloud. After a moment, a second laser flies in (horizontally, from a seemingly arbitrary location) towards the gas cloud to ignite it. The secondary laser might not be able to reach the gas cloud (blocked by terrain/objects) in which case the gas cloud can be ignited manually by firing another shot into it (with the lightning gun or any other weapon that can ignite natural gas) and is also unattainable within the game.
If the target is killed by the second laser or the ignition of the natural gas cloud, perks like Contract Killer and Lawbringer will not be activated (since you didn't actually kill the target).