Flynn's route ending, truly is weird!
From what I can tell and what others have said around the internet, I think it goes like this.
Spoiler!
Flynn started hallucinating when him, Carl and Daxton where at the lake, he could no longer see them. He mentions feeling like someone was tugging on his shirt, that was the other two trying to get his attention. He thinks he went to the smoke room, but he really went to the mine. An evil entity posing as Sydney entered his mind and led him into a fire in the mine. He gets all burned up and Carl and Daxton see him! The entity takes him through time where he loses more of his body until he becomes the monster! If you saw the ending image, thats all thats left of Flynn. He became undead under the control of the evil within Echo.
I could be off, but thats how it seemed to me, very tragic...