Responses
I'm afraid I'm gonna complete your theory and confirm that your guess is probably correct, as much as I don't wanna do it. In mangaka's previous work, Rumspringa, that is a sequel to this storyline, Gene's family still misses him and talks about him as a distant memory, so he definitely did not return back home. Does it mean he's dead, I don't know, I sincerely hope not, but well, here we are.
Okay I have a theory! So they reference the book, “Death in Venice” when Trevor says, “I don’t want to become Aschenbach”
Ref: http://www.mangago.zone/read-manga/dear_gene/uu/d_v-1-chapter-5/pg-6/
In Death in Venice, Aschenbach is an older man traveling in Venice who notices a teenaged-boy, named Tadzio, with his family. He is captured by his beauty and begins following him. Eventually though, a wave of illness strikes the city and Aschenbach chooses to stay instead of return home because of his love. Aschenbach has a dream that he will die in the near future and Tadzio will die shortly after. Aschenbach catches cholera and does indeed die.
As Trevor said, there are vague parallel in the story, so it could be interpreted that Gene died.
Also at the beginning of every chapter, there is a snippet from the journal that says, “Dear Gene, you are my god, eternal love forever”
Ref: http://www.mangago.zone/read-manga/dear_gene/uu/d_v-1-chapter-5/pg-1/
This, of course, call back to when Gene said the same thing to Trevor. The first part could mean anything, but the second part about their love being “eternal” definitely points to Gene having pasted away.
The only thing disputing the Gene death theory is if he returned to living an Amish lifestyle, which I highkey doubt. If you have any additionally theories defo leave a comment, I’m interested in see what other people thought.
Sorry for how love this is (tldr: I think Gene died)