Alright so I think a lot of people are expecting something grander then what this story is.
To put it simply Hikari Tsujimoto is the literal incarnation of the Kudan, the Kudan is the Judge of Japan and he is born through out the history of Japan to judge the Japanese peoples way of life.
This is seen during the Meiji restoration and during WW2 which are both Major times in Japanese history. Both times he decided that humanity needed to be reset and as such there was a great war and the nuclear bombs which both changed the course of Japanese history.
The Meiji restoration put an end to the age of Samurai and feudal lords returning it to it's imperial roots with a single god like emperor who controlled everything which made Japan begin to industrialize very quickly changing the course of Japanese history. The 1930s is when Japanese started to turn ultra horny for resources and wanted to make a name for itself especially after getting fucked over by the west in one. This lead to the infamous invasion of China and Korea as well as all the crimes committed their. The nuclear bombs dropped on Nagasaki and Hiroshima put an end to the imperial age of Japan and created modern Japan.
All of these occurred because the Kudan Hikari thought that their needed to be a reset, the people of Japan were being evil or whatever he's supposed to judge them on.
The Hikari we meet is the modern day Kudan incarnation and a strange Kudan. He's become too attached to this world and isnt doing his job in judging it. He's also not anyone important either. The Kudans power to judge seems based on its importance and popularity. Hikari is the only member of his group to not have a job offer. No one knows who he is, he's just a normal man instead of a well known Samurai or high ranking solider so he has no power.
The Kudan is not happy with the current Hikaris unwillingness to do his job so it instead plants another Kudan into their path which they hit and kill. This way it can slowly chip off those who know Hikari exists being his friends one by one to slowly erase his existence (Which relies on people knowing he exists.)
The Kudan which gets hit by the car the 2nd Kudan is then brought into the physical realm by him having sex with the crazy bitch and creating her crazy baby. Her prophecy's are to get peoples knowledge of the Kudans curse and by extension Hikari out into the world.
It's manipulating Hikari to fall into a situation where he's forced to make his decision which I assume is to save humanity in the end but this isn't his decision entirely.
Chizaru has a role to play in it and so does her father who is the opposite of the Kuzan (Cow head on a human body) and who I'm assuming to be a Vengeful spirit like Sugawa No Michizane. The dad is set on fucking over the Kudans plan to reset humanity. When he dies Chizuru wants revenge on Hikari but instead falls in love with him and making him loose focus of his plan.
I think Hikari breaking past the fence as a kid and running into the road is symbolism for him breaking free from his role in the Kudans plan. Also the reason his shadow returns is because that video tape of him being immortal is shown around so he's pushed back into the lime light and people know he exists on a basic level.
I assume Chizaru loosing her shadow is not to erase her but put her into the position she's in at the end. The Kuudan was playing the long game which is why Hikari at the end realizes he fucked up and says he lost. He fell right into the Kudans plan and is forced to make his choice.
I think the final chapter shows that becase Hikari didn't reset humanity like he was supposed to a new Hikari is summoned to restrart the process. The reason Hikari was erased is because Chizaru died so all his friends who knew him at the start were gone and his idneitty was forgotten.
No one else knew him as anyone other then the Immortal man or the naked streaker. Only his friends knew who he really was and as such with them gone he was erased.
This is something I'm really pulling out of my ass here though, just me connecting the dots in my head. There's some other stuff like the Goto islands being mentioned which were somewhere Japanese Christians moved to after the main land started prosecuting them so if I knew more about that history I could probably connect the dots easier to the Christian girl. I'm also probably missing a lot more due to the poor translations and my surface level understanding of Japanese history so feel free to submit your own thoughts.