Ultimate Spider-Man Clone Saga
The Clone Saga was adapted for Marvel's Ultimate imprint. It began in Ultimate Spider-Man #97 (July 2006) and concluded in #104, with a small epilogue in #105. In the Ultimate Spider-Man continuity, the character Miles Warren was first introduced as Harry Osborn's psychiatrist who was hired by Norman Osborn to brainwash out any memories of his Goblin persona. Ben Reilly was established as an African-American lab assistant with no personal ties to Peter. Although in the "Carnage" story-arc, Reilly refers to the Carnage creature as "Little Ben". The creature itself being created from Peter Parker's and Curt Conner's DNA with traces of the Venom suit's genetic material as well.
In this version, Bendis wrote a story in which the Ultimate Scorpion is captured and revealed to be Peter's clone, sharing 94.2% of Peter Parker's DNA (issues 97, 98). MJ is then abducted, and searching for her, Peter runs into Ultimate Spider-Woman, and in the following issues, further Spider-Man clones appear, among them one with a disfigured face (Kaine) and a black-suited clone with six arms (Tarantula). Bendis also made Peter reveal his secret identity to Aunt May and the Fantastic Four, and let an amnesiac Gwen Stacy and Peter's presumed dead father Richard re-appear (though the former of the two actually escaped). Via a longer dialogue through Peter and Spider-Woman, Bendis also established that every clone has inherited Peter's love for MJ, and his worries of her getting hurt; as a result, they each tried a different approach, the Scorpion trying to make sense of his jumbled memories, Spider-Woman trying to stop the other clones, Kaine using his advanced mind to incorporate the drug OZ into MJ's body, and the Tarantula trying to defend MJ from Kaine.
Upon waking to find that she has been injected with OZ, MJ is enraged, and her anger triggers a transformation into a large, red monster. As of issue 103, the masterminds behind the clones seem to be Dr. Octopus and Ben Reilly (Reilly stole a sample of Peter's blood shortly after the death of Gwen Stacy). A fight between the clones and Dr. Octopus leaves the Tarantula and Kaine apparently dead, and Dr. Octopus captured by S.H.I.E.L.D. As a twist, Bendis established that Dr. Octopus and Reilly acted with consent of the FBI. In addition, Gwen is revealed to be Carnage, and Richard revealed to be yet another clone (issues 99-103), aged artificially and given psychic treatment to create his false memories.
As of the end of the Ultimate Clone Saga, the clone posing as Richard Parker died from his rapid aging, Jessica Drew fled after helping Peter defeat Octavius, and Doctors Franklin Storm and Reed Richards found a cure for Mary Jane's OZ-related affliction; Peter's relief at her safe condition made him realize his true feelings for her and resumed their relationship. Reed Richards suggested that they might even remove Peter's powers after some more research, since they are also partially caused by the OZ serum. However, after a talk with Nick Fury, Peter rejects the cure and got back together with MJ. The Spider-Woman clone left to embrace the "Jessica Drew" identity and the other remaining clones—the Scorpion and Gwen Stacy—were left in the custody of Nick Fury, who advised his Scientists to 'get to work' on them.
In re-imagining the story for the Ultimate Universe, Brian Bendis inserted many references to the original Clone Saga. Among them are that the brief appearances of the characters Miles Warren and Ben Reilly; Peter re-examining his relationship with MJ; an amnesiac Gwen Stacy appearing from nowhere, then turning out to be more than she seems; Aunt May experiencing a heart attack; a "Scarlet Spider" (Spider-Woman) evading Peter and later being used as a plot dump; a half-formed, semi-insane clone appearing several times, specifically wanting to protect MJ; a 'mystery woman' called 'Jessica'; an old friend and colleague of Norman Osborn appearing to have been manipulating the scenes from behind (Dr. Mendel Stromm in normal Marvel continuity, Otto Octavius in Ultimate Marvel continuity), later revealing unseen powers over metal.
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