I don't mean to ruin headcanon, but going but what we know of the Omnitool, it's almost 100% sure she is dead, and since that was the only known chip of her and a unique AI persona, I do think that leaves Simon all alone... Unless he left other people alive through the game ironically, I don't think they would of died in the day or so he was gone, so ironically the people he left alive during the game may be his only company if he can reach them.
Though obviously the big point of the ending is consequences in such a system and heroics. Simon, as we play him, is actually the third Simon of four we play as (since we play his human memories at the start, then play the first diver suit, then the second diver suit, then the Simon in the ARK), but from his perspective he's gone through the whole journey, to save humanity, and clings to a dream that he'll live in a perfect world at the end of this nightmare, and loses his lid when he realizes that, for him as he is now, there's no escape. But as he takes it all out on Catherine, she stresses out too much and dies due to being linked to too simple a virtual system (as we see earlier how that's calculated in virtual space through the puzzle involving the man who stresses out too quickly), and Simon comes to realize the last thing he ever said to her made them end off badly, and now he is all alone at the bottom of the sea. It's a dark ending, but I think that's the point, he worked hard for this and he made ARK, the last 'living' trace of humanity, to go on to survive thousands of years, but he himself, from that perspective, as that self, as well as the Simon before him, is unrewarded. He did a good thing, and the sacrifices he took was for this good thing, in the end he himself gets no personal gain out of this. I think personally judging off of Simon's personality and how he thinks of things he likely commits suicide, he has quite a personality that overthinks and dwells on things, and I don't think he could cope being alone at the bottom of the ocean with no hope.
Meanwhile, the other Simon is the definition of ignorance is bliss, to him the procedure worked without a flaw, and now he gets to be rewarded and live a dream life along with Catherine, who he's bonded with. They succeeded, they were rewarded, and they get to live out the rest of their lifespan happily (probably).
I admit I've thought about this sort of thing before, if such things as alternate realities exist, then there's thousands to millions of moments that we die at any moment from any method of possibilities, in some branched 'what if' possibility, we were killed brutally in some incident, but we ourselves as we are know nothing of this and could live blissfully in that fact where other 'versions' of ourselves have died.
