This being my favorite Spider-Man show, ever, of all time, I think that this problem hits me twice as hard as the others. I heard somewhere that he was going to find MJ in London, modeling, with her memories erased. Also, if Spider-Man Unlimited was a loose continuation of this series, as it is often said to be, then one could assume that he did eventually find her. But the thing is we'll never know for sure. As far as I'm concerned, Peter and Madame Web are still lost in a void of reality, searching for, but never finding, Mary Jane Watson.
That ALWAYS bugged me!! We’ll never know how it ends!