The storyline is one of the most controversial Spider-Man stories ever told. Although it was supposed to wrap up in less than a year, the comics sold very well, which caused the writers prolong the saga as long as possible. This led to some changes to the storyline that were ultimately disapproved of by fans.
The First Clone Saga
The Jackal was the secret identity of Gwen and Peter's biology professor Miles Warren, who could not cope with the death of his secret love, Gwen. As an expert on cloning, he creates clones of both Gwen and Peter, discovering Peter is Spider-Man as a result. Jackal blames Spider-Man for Gwen's death and wants to kill him. The Jackal kidnaps Spider-Man and forces him to fight his clone. Both men believe they are the real Peter Parker. The two Spider-Men soon decide to work together, but one is seemingly killed by the same bomb that kills the Jackal. The surviving Spider-Man determines he is the original because he is in love with Mary Jane Watson, which didn't happen until after Prof. Warren created the clone. Spider-Man drops the body of the clone into an incinerator. Gwen Stacy's clone disappears to find a new life for herself.
A few years later, Spider-Man encountered Carrion, who claimed to be a degenerated clone of Warren. The clone of Gwen Stacy reappeared many years later when she was being pursued by the High Evolutionary, who was determined to discover how Warren had been able to perfect cloning. In the process, he discovered that Warren had not, but had instead created a genetic virus which transformed already living beings. "Gwen Stacy" was seemingly cured of the virus and left to lead her own life once more.
Later, Spider-Man investigated Warren's old laboratory and discovered that Carrion had in fact been a genetic weapon created by Warren. Another former student of Warren's, Malcolm McBride, became infected with the virus and became the new Carrion. After that, with Scarlet Spider Unlimited #1, this story arc was molded to fit into the New Clone Saga.
The Second Clone Saga
More years passed before Spider-Man's clone reappeared. He had survived the battle and for five years had lived an existence under the name Ben Reilly (a combination of Peter's Uncle Ben's first name and Aunt May's maiden name). A series of chaotic events followed, in which Peter and Ben were plagued by both a resurrected Jackal and by Kaine, who was an unsuccessful first clone. In the process, another clone of Spider-Man became the villain Spidercide. Matters were further confused by the interventions of the mysterious and seemingly all-powerful Judas Traveller and Scrier.
Medical tests indicated Peter was actually the clone and Ben the original. Peter temporarily retired as Spider-Man, leaving the mantle of Spider-Man to Ben while he prepared for his new role as a father after the discovery that Mary Jane was pregnant; Peter even lost his powers for a time during his 'retirement', although they eventually came back after a near-death experience. An explosive climax revealed that Peter, Ben, the Jackal and many others had all been manipulated for years by Norman Osborn, who had returned from the dead and had been secretly masterminding the entire saga all along. Osborn said Peter was the original, having faked the evidence that revealed Peter's status as the clone as part of a plan to break Peter's spirit. This claim was confirmed when Ben died saving Peter's life and his body degenerated like any other clone's. Spider-Man: The Osborn Journal (February 1997) explains the Green Goblin's role in the entire storyline.