Scordopordonicus

Simon's universe is just a precursor of Ryland's. There was that, then billion of years pass- how do we get Simon though?

The seed he was carrying fell into the blood ocean when the eel attacked him. The blood of the blood moon turns out to be a super fertiliser/growth stimulant. The current carries Simon's body away from the eel just enough not to be eaten (the bottom is unstable and all that right) and the tree almost immediately grows AROUND Simon's body, sets roots in the blood moon and keeps growing for billion of years.

Then one day, Ryland Grace and Rocky are going back to Erid, and stumble upon a moon that has traces of biological matter, a giant skeleton, and a tree. Maybe it's dying. They use the dead moon as a pit stop to breed more astrophage (they know how and can as long as they stop the Mary and extract some astrophage from the fuel reserve, cue Ryland and Rocky building a Venus-b room to produce astrophage, cutesy parallels and also painful memories for Ryland) to go home faster.

And the tree somehow opens, and a thing falls out. A human shaped body! Or maybe the landing of the Mary tears the already week roots and the tree finally dies, and as it falls it breaks and by some sheer miracle Simon's body makes it out in one piece. He's malnourished and weak but Ryland immediately puts him on the Mary (also Simon might have been modified by the tree to breathe in the atmosphere, which would create the need for yet ANOTHER atmosphere on the Mary and drive the touch starvation up the wall).

So billion of years later, Simon is the last survivor of the "humans" that came before the current humanity. Speculations on evolution are made, but point is there isn't a "I left my universe", his universe died. His whole mission was for nothing. He "died" for nothing. Radiate him with survivor's guilt.

...also I like the idea of a blood eating tree sustaining Simon. The blood ocean is already ominous, imagine a tree, symbol of life, feeding off the blood ocean to the point of drying it over the billions of years. And also, the whole "our bodies become the soil" being subverted, the tree protected Simon's body (though it would be for survival reasons, in a symbiotic relationship- for what? idk. Body horror that man and make his lungs be the tree's lungs maybe).

Live long and be gay

Revelations 16:3