* AuthorsSavingThrow:
** In the case of the First Clone Saga, Creator/GerryConway, who was worried that his over-the-top story about clones and Jackal was a little too quirky for Spider-Man, later wrote in ''The Spectacular Spider-Man Annual #8'' during the crossover event "The Evolutionary War" that Miles Warren never actually cloned anyone. What the Jackal did was create a drug and experimented on a woman who had some of Gwen Stacy's attributes, with his cocktail altering her to genetically resemble Gwen. In other words, Jackal never actually cloned anyone, what he did was mutate subjects into clones. Conway saw this as a way to {{handwave}} how exactly the Jackal, a lowly college professor at ESU, was able to make a breakthrough in human cloning (he didn't), clarify and explain away the fate of the missing Gwen clone, and once and for all put to rest the idea of Spider-Man being any kind of clone. [[note]]Years later, this too was retconned to "Jackal actually ''did'' create legit clones, and all the stuff that said he didn't was made up by the High Evolutionary, whom Warren had worked with in his earlier years, to discredit him because some of his beast men were viewing him as a god-like figure and he didn't want that."[[/note]] Glenn Greenberg, who wrote the "Life of Reilly", expressed frustration at Conway for, as he put it, going "to great lengths to undo his own stories", plainly ignoring the memo that Conway felt that clones and the Jackal were both bad ideas beyond one-and-done stories.
** A few were built into the story, but they were never used properly as the collection of writers and editors battled for turf. [[WhatCouldHaveBeen A lot of ideas were bandied around]] and it's debatable if any of this would have truly worked in any capacity:
### Seward Trainer, the geneticist who claims that Peter is the clone, was mentioned as having past history with the Jackal; therefore, everything he says is unreliable. (Incredibly, Editorial vetoed this seemingly obvious exit route.)
### Ben Reilly is revealed to be the clone and melts away. Mary Jane ''also'' disintegrates, revealing that the Jackal had replaced her with a clone long ago, and that Peter was never married to begin with. (The idea that Peter had married a clone of Mary Jane was used to undo his marriage in ''Spider-Man: The Animated Series'')
### Ben and Peter get caught in an explosion; one of them dies; the surviving one has [[AmbiguousCloneEnding amnesia]] and can't be certain if he's the fake or not. Repeating what they thought was the situation in 1974, except without the larger thematic point that ultimately won out there.
### PredestinationParadox: Peter is sent back in time five years, loses his memory, and is led to believe that he's a clone, thus becoming Ben Reilly. Judas Traveler and Scrier ([[DramaticUnmask actually Mephisto]]) are revealed to be responsible for the loop, as part of a CosmicChessGame to see whether good or evil win out.
### Peter and Ben are ''[[DebateAndSwitch both]]'' clones. The real Peter Parker has been held in [[HumanPopsicle cryogenic captivity]] by the Jackal since the first Clone Saga ended.
### Ben dies saving Peter's life at the hands of the BigBad. Back in Portland, Mary Jane miscarries, blames Peter, files for divorce.
* CreatorBacklash:
** A lot of people involved weren't happy with how the story was going, and this resulted in quite a few changes in direction.
** Creator/TomDeFalco, the editor-in-chief at the time the Clone Saga was pitched, thought it sounded like a bad idea right from the start, especially the idea of replacing Peter Parker with Ben Reilly, which he thought readers would never accept. But the Spidey writing team were enthusiastic about it and he, reluctantly, agreed to it on the proviso that a backdoor be inserted to undo the whole thing if, and when, audiences revolted at the story. He ended up losing his authority when sales and marketing were given say over him and that extended the saga interminably.
* CreatorsFavorite:
** It's pretty clear that Kaine was intended to be a BreakoutCharacter, with the writers taking every opportunity to show how powerful and take-no-prisoners he is. Readers instead dismissed him as a cookie-cutter NinetiesAntiHero who had little in the way of actual personality and was needlessly-violent even by the standards of the '90s. That he managed to kill fan-favorite villain Dr. Octopus with minimal effort doesn't help.
** The writers admit to being personally fond of Jack, whom they regarded as PluckyComicRelief that was much needed for such a grim and gritty storyline. Unfortunately, readers who already had a hard time taking the storyline seriously instead saw Jack as a pointless distraction. Writers' attempts to make readers sympathize with Jack (such as his grim realization that he'll soon undergo CloneDegeneration, or his genuine mourning over another clone that was [[TheFriendsWhoNeverHang apparently his friend even though they never really interacted before that clone's death]]) did little to alleviate it.
* CreatorsPest: [[https://lifeofreillyarchives.blogspot.com/2008/03/part-1.html According to Glenn Greenberg on Life of Reilly]], the writers didn't care much for Judas Traveller, due to the fact very few on the writing crew knew what to do with him, and more or less [[WritingByTheSeatOfYourPants having to make it up as they went along]].
--> "No one -- not the writers, not the editors -- seemed to know who or what the hell Judas Traveller was."
* ExecutiveMeddling:
** The series was prolonged due to sales, causing the quality to take a dive. The Clone Saga had the misfortune of debuting during a regime change in ''Marvel's'' editorial staff; the high-earners (Editor-in-chiefs who managed to boost sales during the comics recession) were kept on; losers found themselves demoted or downsized. This ''Glengarry Glen Ross'' approach put extra pressure on editors to prolong the Clone Saga event, even if it meant [[TheChrisCarterEffect dropping meaningless hints and clues]] to tantalize readers. Consequently, several "back door" escape routes were proposed and rejected (see below). The end result was that the Clone Saga, intended to dispel the [[MediaNotes/TheDarkAgeOfComicBooks dark, brooding]] tone of the '90s Spidey books and go "back to basics", ended up becoming the darkest and [[ContinuityLockOut most impenetrable]] story yet.
** Not to mention that, like ''ComicBook/OneMoreDay'', it was an attempt to return to the days when Spider-Man was single.
** The famous [[http://lifeofreillyarchives.blogspot.com/ Life of Reilly]] details what went on behind the scenes, but long story short, what prolonged it was greed (despite the criticisms and mocking it gets, [[CriticProof it]] ''[[CriticProof was]]'' [[CriticProof making Marvel money]]), attempts to recreate the success of [[ComicBook/AgeOfApocalypse another storyline from the same time]] (hence the "Maximum Clonage: Alpha and Omega" one-shots and the ''Scarlet Spider'' titles for a few months), [[TroubledProduction trouble behind the scenes]] over where to go with the story, and not wanting the finale to compete with the ''ComicBook/{{Onslaught}}'' storyline.
* ExecutiveVeto: This happened enough times that it almost belongs under Executive Meddling. Among the story threads that were shot down: Ben adopting Peter's identity after the latter passed away (leaving the Spider-canon more or less the same), one Spider-Man dying in an explosion while the surviving one [[AmbiguousCloneEnding loses his memory]], and (wait for it...) having Mephisto erase the whole thing via a CosmicRetcon.
* FollowTheLeader: The return of the clone and debut of Kaine follow the wave of "[[AntiHeroSubstitute replace-the-hero]]" comics started by ''ComicBook/TheDeathOfSuperman''. Additionally, the "Maximum Clonage: Alpha and Omega" one-shots and ''ComicBook/ScarletSpider'' titles were inspired by similar gimmicks in ''ComicBook/AgeOfApocalypse''.
* LyingCreator: Some fans think this of the "director's cut" miniseries. It's hard to write a story as "originally intended" or having a single director's cut when you had multiple creators and writers with separate ideas and plot thread going in different contradictory ways. J. M. [=DeMatteis=] one of the collaborators for it, for his part sees it as faithful to how he and others saw it (namely allowing an older Peter an ending with Ben Reilly as his LegacyCharacter and successor), while others such as Gleen Greenberg point out that a plan was to have Peter return to single status at the end with Mary Jane leaving Peter over the trauma of their miscarriage (which writers nixed because divorce compromised Spider-Man's optimistic image).
* MilestoneCelebration: The saga was [[WhatCouldHaveBeen originally]] planned to end at ''Amazing Spider-Man'' #400, with Peter PutOnABus and Ben becoming the new Spider-Man. Thanks to ExecutiveMeddling, however, the story arc ended up going on for far longer due to its popularity. That said, ''ASM'' #400 was notable for Aunt May's heart-rending passing and many still consider it, on its own merits, a classic story.
* ReferencedBy: As the first episode was a review of the "Smoke and Mirrors" arc, ''WebVideo/AtopTheFourthWall'' had a storyline that did its own spin on this for its tenth anniversary, though [[spoiler:it's also a case of NeverTrustATitle as the "clone" is really Mechakara CameBackWrong and the true villain is {{Mirror|Universe}}kara; the latter having killed the real clone to test an AgonyBeam.]]
* ScienceMarchesOn: A very odd example occurred during this story--in the '80s and '90s, some scientists started to believe that cloning was impossible, and for some bizarre reason the writers of an outlandish superhero comic decided that this "fact" undermined the entire clone saga and needed to be addressed, so Miles Warren was retconned[[note]]prior to the actual '90s Clone Saga, but the story brings it up anyway[[/note]] into actually creating a weird sort of virus that rewrote the DNA of captured individuals so that they became copies of the original and then wiped and somehow rewrote their memories so they were not ''actually'' clones... which got very awkward a few years later when scientists successfully cloned sheep and other animals, thus disproving the idea that cloning was impossible. To make it more awkward still, neither any virus nor actual human cloning would have the precise effects that the Jackal's cloning efforts are portrayed as having (real-life clones are more like glorified identical twins, for instance), so both explanations were always pure science fiction anyway.
* TroubledProduction: Very much so, as documented in ''Life of Reilly''. It's part of the reason the storyline dragged on so long and ended up as such a convoluted mess.
** Shortly after the arc began, Marvel's financial problems began to bite: editor-in-chief Tom [=DeFalco=], who had greenlit the whole thing, was fired, and Marvel's comics division was divided up and restructured. This meant that a lot of key personnel involved in setting up the Saga in the first place were no longer there to help steer things in the intended direction.
** ExecutiveMeddling forced the writers to keep stretching the storyline out which, combined with the aforementioned lack of direction, led to writers throwing plot threads at the story seemingly at random, just to pad things out and try and keep readers engaged. JM [=DeMatteis=], one of the lead writers for the Saga, soon resigned after suffering from creative burnout and running out of ideas.
** [=DeFalco=]'s replacement, Bob Budiansky, was eventually convinced by [=DeMatteis=]' replacement, Dan Jurgens, to reverse course and reinstate Peter Parker as the real Spider-Man... except that nobody had any idea how to actually do that without it looking like a blatant cop-out. While various ideas were proposed (see WhatCouldHaveBeen below), the writers and editors couldn't agree on an approach, and the resultant stalemate meant the arc dragged on ''even longer''. Finally Jurgens came up with a proposal that Budiansky seemed to like, stating in a memo, "This is my last shot. After this, I give up." Before work could begin on it, however, Marvel underwent ''another'' restructure and Budiansky was replaced by Bob Harras, who ordered '''''another''''' delay so the conclusion wouldn't clash with the planned "Onslaught" story arc. True to his word, [[ScrewThisImOuttaHere Jurgens quit]].
* WhatCouldHaveBeen: A ''lot''. They can all be read on the ''Life Of Reilly'' article. A few notable ones, some of which were uses in the 2009–2010 "director's cut":
** At one point no-one was the clone, and in fact Peter and Ben were the same person caught in a StableTimeLoop. When this went against Marvel time travel rules, it was decided that someone was needed who could plausibly ignore said rules. So Scrier was going to be [[ComicBook/OneMoreDay Mephisto]], and he was going to trick Peter Parker into going back in time and becoming Ben Reilly in order to gain the soul of Judas Traveller, who was going to be a FallenAngel. This was nixed for [[HilariousInHindsight many of the same complaints against]] ComicBook/OneMoreDay.
** Another was that the character Gaunt would be the mastermind, with the idea being that the real mastermind was [[BackFromTheDead coming back from the dead]] inside Gaunt's costume, although they weren't initially sure who Gaunt would be. Eventually they decided Gaunt's identity would've been Harry Osborn, but this was felt to be too much like a previous story where Harry [[ThanatosGambit posthumously]] made robotic duplicates of Peter's parents. This led to them going back to the drawing board and making the mastermind not be Gaunt, which drew out the story even more. The mastermind became Norman Osborn, while Gaunt eventually turned out to be [[UnexpectedCharacter Mendel Stromm]].
*** The "director's cut" mini-series used the idea of Harry as the mastermind, albeit having Harry faked his death rather than actually dying and coming back.
** The ''Final Adventure'' mini was supposed to retire Peter as a superhero and MJ give birth to their daughter. Before the final issue was completed, everyone involved knew Peter would resume being Spider-Man, so Marvel wanted the mini to end with MJ having a miscarriage instead. Editor Tom Brevoort refused, the ''Life Of Reilly'' even quoting him as saying, "There's no way in hell that I'm going down in history as the man who killed Spider-Man's baby."
** And yet another one was that Eddie Brock was going to replace Peter as Spider-Man using this as a way to bury the hatchet on their rivalry and Ben would've kept being the Scarlet Spider. The reasons for not doing this was because they were scared of making Eddie not ComicBook/{{Venom}}.
* WordOfGod: The ''Life Of Reilly'' article features commentary from people involved in the Clone Saga, including revealing bits that didn't make it into the story such as Kaine's costume featuring a Life-support system and as a result of the defects in him, his PsychicPowers and Mark of Kaine were just amped up versions of Spidey's Spider-Sense and wall-clinging abilities.
* WriterRevolt: Veteran Spider-Man writer Tom [=DeFalco=] was often said to be particularly displeased with killing off Doc Ock, and he unfortunately wound up being required to write that issue. First chance he got after the saga, however, he brought Ock back. He also didn't like Gaunt and seemed to try to kill him off as quickly as possible. Similarly, regarding both of them, when doing the alternate universe miniseries, he just opted to have Ock survive his encounter with Kaine and have Harry come back without the idea of him being Gaunt.
* WritingByTheSeatOfYourPants: There wasn't really a single writer or writer-artist team behind the project (unlike the original clone saga by Creator/GerryConway which had a clarity of intent and purpose[[note]]Chiefly that Gwen Stacy was gone and it wouldn't be the same if she came back, and Peter and MJ are made for each other which was what that entire story was about[[/note]]), instead there was a story by committee, where each group and individual had no idea where to take it. EIC Creator/TomDeFalco tried to give it direction and ensure there was a way to undo what he saw was a short-term gimmick and project at best, but once marketing and sales took over and he stepped down, the entire project went out of control. According to legend, at one point when considering how to end the project, ideas were pitched not only to the Spidey team, but all of Marvel, and even the janitors, office clerks, and non-creatives were asked for their opinion.
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