The story becomes very easy to understand if you pay attention to the first page (not the credit one). And have your monitor zoom in because once I did that everything becomes clear.
My take: A lightning has struck a plane with full of students aboard (while accidentally scraping it). Guilty, the lightning decided to hold on on the only survivor, a boy called Mirai. In order to not arouse suspicion for when the boy wakes up, the lightning used its static properties to gather "materials" in order to form a humanoid body. When the boy woke up, the lightning tried guiding the boy to a safe place (lighthouse), but the boy grew affinity towards the lightning and wanted to share the little last source of energy he had (a package of sugar with the same name as he) despite being weak. He opens and drops down the sugar satched, and lightning tried to grab it, but it causes a reaction and lightning's arms started to fall apart, he then tries to block the boy's view from seeing his actual self with a bandage, and progressively his body starts to break down and he went back into being immaterial, then went into hiding until he can build a new vessel. The boy wakes up from his half-asleep state, and started looking for the lightning, he eventually ventures near a cliff and falls down (not sure if inntentional or not---perhaps suicidal or he wasn't thinking straight due to lack of nutrition). then lightning catches him, but this time he did not have a proper vessel ready, the boy ends up charred down. realizing what he had done, lightning started to use all his hands to catch what's remaining of the boy, but to no avail. A storm starts to rage on a a terrible downpour followed by an intense lightning rod (I guess they can call it the cry of lightning). Once the sky is clear, a girl was found shipwrecked and lightning guides her to the lighthouse.
tl;dr: accident, accident, accident.