The headcanon/idea I came out today is that Simon does survive the explosion of the submarine that killed The Eel, but he becomes a new kind of monster, a more humanoid version of The Eerl, with fragments of the tree implemented on his body, but still not longer human.
No memories, no feelings, no humanity, or purpose besides his duty of protecting the blackbox from other creatures that may live in the Blood Ocean. He can't remember why, but he has to protect the remains of a rusty, destroyed submarine that keeps sending a frequency in loop, and that little box floating in the middle of nowhere.
Once a human takes the blackbox- because he can still recall humans, at least the idea of them, how cruel they are, how violent and yet, how much they meant for him- any remains of Simon's mind get lost, now free of his duty and he just becomes one more of the things lurking under the surface (because he slowly stops been a he, he slowly stops been Simon and it becomes something else).
Extra (Scene? Idea? Scenario?) + Grace and Rocky
After going fishing and produced the taumeba, Grace and Rocky may have caught a frequency coming from a small moon, and thinking that it may be another form of life asking for help with the issue with the astrophage they get close to see.
The atmosphere of the moon is pretty similar to the one in earth, or Luna (earth's moon) so Grace and Rocky can get in the moon and do a more close investigation.
They found a moon made my blood oceans, and confused they keep serching until they found a blackbox floating in an old and raggy life jacket. Rocky can't riskied to get of the Hail Mary, he could sink so is Grace who has to go aout and take it.
Imagine Grace having to swing in the Blood Ocean with his EVA, and he feels something brushing against his feet, and he screams but he refuses to leave the blackbox so he just swim faster to get the box and when he finally has his hands over it he looks up and finds himself face to face with Simon, or whatever it is left of him.
A human head, with very little, completely black eyes, just poiting teeths, with skin that seemed to have been melted from the inside out, with blood all over it.
Grace freezes, all the alarms sounding in his brain, but too scare to move, fearing looking threatening. Simon puts his webbed hands over the blackbox and he looks at Grace.
Simon had been waiting for so long, clinging to his humanity in this form was so hurtful, a reminder that he wasn't human anymore, that he had become something...else, but he had a duty and finally an angel have come down from the skies to free him from having to guard this blackbox. Simon can finally let go.
He then pushes the box to Grace's chest so Grace can have a stronger grip of it and when Simon can see the blackbox safe on Grace's arms, he murmurs:
"It's bigger than me." Talking is hard with all the new teeths in his mouth, and his voice is too raspy due to disuse, but Simon feels he has to say something. "Thank you".
And Simon just dives in the water to never been see by a human eye ever again, having the freedom to let go of those last parts of Simon that reminded him that he was a human once and he can finally embrace his own oblivion and being just a monster.
He is saved, but it isn't a happy ending
Grace takes the blackbox and makes sure to transmit its information as far as he can, including it in the bettles too, and after that Grace just breaks in tears.
