Since Hydro Man was created a while before Mary-Jane, he should have evaporated much sooner than her instead of just before.
Spider-Man: (as he sits on top of the bridge) What happened to you Mary Jane? I can't go on without knowing. Not as Spider-Man! Not as anyone!
Madame Web: (as her presence is known) Oh how wrong you are Spider-Man as usual!
Spider-Man: (as he ends up in a vortex): No, not you again!
Madame Web: I still have something very important for you to do. Have you forgotten I was preparing you for this longwhile for the most important battle of your life?
Spider-Man: I remembered all of my encounters with you Madame Web. I want nothing to do with you.
Madame Web: But suppose I told you I know where Mary Jane is and you will only find her if you do as I command.
Spider-Man: (as Spider-Man swirls through the vortex) Leave me alone!
Madame Web: I cannot! This is your destiny, Spider-Man. And now the fate of mankind rests on your weary shoulders.
Mary Jane: (To Hydro-Man) I hate the sound of your voice, I can't stand to look at you...
Spider-Man: And let's not bring up your personality!
Spider-Man: What happened to you, Mary Jane? I can't go on without knowing-- Not as Spider-Man... not as anyone.
Mary Jane: Before I go I want you to know just one thing. If any part of me is anything like the real Mary Jane Watson she loves Peter Parker more than anything in the world-- more... than... anything.
Miles Warren: I'm afraid I have some rather unpleasent news. The latest blood tests on Hydro-Man have shown that the cloning process has proven unstable. You're coming apart just like my first clones. It has just taken longer to happen this time. According to my research neither of you has much time left.
Mary Jane: I remember... suddenly finding myself at the bottom of the bridge and seeing Spider-Man battling the Green Goblin. But I don't remember falling off or anything that happened in between. Oh, I hate this bridge.
Peter: Me too. Whenever I'm here, I feel like something bad is going to happen.
Hydro-Man: Kid, you oughta become a psychic!
Miles Warren, is infamous for creating the Spider-Clone in the comic books. Warren is also known as the Jackal. Jonathon Harris, who plays Miles Warren in this episode, also played one of the classic evil scientists - Dr. Zachary Smith on the original "Lost In Space".
This is very similar to an episode of Lois & Clark: The New Adventures of Superman. In both cases, the hero winded up marrying a clone of their girlfriend who winds up dying trying to save them. Only Superman does reunite with the real Lois Lane.