guy loses daughter in an outbreak of some plant that(in real life only affects ants I forget the specifics but this plant is real, just not like the one in this game) has mutated way way beyond what it originally was and affects humans, turning them into violent monsters with gross fungal growths all over their heads which eventually spreads all over their bodies
20 years later guy is experienced smuggler and is tasked with smuggling some girl across his town
turns out girl is immune to the plant disease thing, making this mission much much more serious
blah blah follow the fireflies blah blah
he eventually finds that this girl he has been tasked with escorting he ends up loving as if she replaced his missing daughter
in the end they reach the fire flies and guy finds out that they intend on removing her entire brain to develop a cure which would kill her
he says FUCK THAT, kills almost every last one of them grabs the girl and proceeds to leave, where he is confronted by the fire flies leader(the person who originally tasked him with escorting the girl)
you then see him driving away thinking he gave the girl up and let them kill her to save humanity but NOPE! she then makes a noise and it scoots back to the cutscene showing the leader, where he mercilessly kills her and takes off, leaving humanity in the state it will be in forever supposedly
in the end she asks him if everything he had told her was the truth regarding that incident as she was knocked out during the entirity of the end part, he lies and tells her it was the truth, she says ok
roll credits