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The Return of Hydro-Man is a TV Movie in the 90's Spider-Man series from season 5.
Mary Jane and Peter arrive in Niagara Falls for their postponed honeymoon, but it is soon interrupted when Hydro-Man (last seen in season 2) returns and kidnaps Mary Jane, with Spider-Man and the Black Cat in pursuit (she's taking a break from her travels with Blade and Morbius). After some intense detective work, Spider-Man tracks down Hydro-Man to a water factory in New York. Hydro-Man has Spider-Man beat, until someone clobbers Hydro-Man with water powers, and that person is Mary Jane!
There's no answer for Mary Jane's new found water powers, until Spider-Man follows Hydro-Man to his under-water lab..... only it turns out she's really a clone, and so is Hydro-Man. It seems that Alistare Smythe hired Miles Warren to use his cloning technology, except it wasn't perfected. Basically as a test, Warren went to the place where Hydro-Man "died" and took a cell from the water type substance. So, a Hydro-Man clone is born.
When Hydro-Man read a paper involving Mary Jane's disappearance, he told Warren to make a Mary Jane clone. Warren went to her apartment and got a hair strand from her comb, before the accident. The Mary Jane clone is made, but she flees Warren's lab (the same one used by Norman Osborn, the Green Goblin) and finds Peter. After Spider-man's final battle with Hydro-Man, Hydro-Man and Mary Jane degenerate, and Warren flees, with a part of Spider-Man's costume. Spider-Man's alone again. Suddenly, Madame Web plucks Spider-Man away. She tells him that the time has arrived, and that he must do her bidding since she knows where the real Mary Jane is.