"To read the Clone Saga from beginning to end is to watch the total systematic failure of Marvel’s editorial and publishing practices at the time. The result has a horrible grandeur unmatched by any other ‘90s comic book spectacle."
The Clone Saga (or Spider-Clone Saga) is the name of two Spider-Man story arcs, one from the 1970s and another running from 1994 to 1996, both involving Spider-Man and clones. The second story, which is a sequel for all intents and purposes, is better remembered for being one of more the contentious Spider-Man stories — ranked up there with Sins Past and 'Comic Book/'One More Day'' — and the only time in history when the words "Maximum Cloneage!" could be printed unironically. Intended to wrap up in less than a year, the comics sold well enough that the writers were 'encouraged' to prolong the series as long as possible. This led to some changes to the storyline that ultimately proved very, very, long.The first Clone Saga was primarily written by Gerry Conway. The second Clone Saga is most commonly associated with Terry Kavanagh, though many other writers were involved in the project, among them: Joey Cavalieri, Todd Dezago, J. M. Dematteis, and Tom Defalco.
The nineties Clone Saga follows the reappearance of the Spider-Man clone, apparently Not Quite Dead when Peter disposed of his body, who has built a new life for himself and taken up the name Ben Reilly (after his Uncle and Aunt's first and maiden names, respectively). The details of this story, including behind the scenes information can be found in the site The Life of Reilly, which may be a book someday.A brief summary: The Jackal comes back and starts playing mind-games with both Peter and Ben. A new villain, Kaine, is introduced and is eventually revealed to be yet another clone of Spider-Man; in fact, the first one made. He eventually becomes a Nineties Anti-Hero in an attempt to make him the breakout character. Mary Jane gets pregnant. Aunt May and Doctor Octopus die. New villains are introduced such as Spidercide, Judas Traveller, Scrier, and the second Dr. Octopus. The Jackal also dies, but not before it is "proved" that Peter Parker is the clone and that Ben Reilly was the original Spider-Man. Though initially crushed by the news, Peter decides to hand the mantle of Spider-Man over to Ben so he can start a family. Fans and writers united in an uproar, and an Author's Saving Throw was developed (there were a few built in there originally, but were never used as intended), revealing that Peter really was the original Spider-Man and the whole thing was manipulated by Norman Osborn, also back from the dead. In the end, Ben Reilly died in a manner that explicitlyshowed he was a clone, the Green Goblin returns to being Spider-Man's archenemy, the Clone Gwen disappears again, and Aunt May and Dr. Octopus also come back from the dead because mumble mumble reasons. Oh, and Mary Jane miscarries (or does she? Read Spider-Girl for more details).In the end, for the most part nothing was changed.Elements from the Clone Sage were twice integrated into Spider-Man: The Animated Series, once with Mary Jane being the one cloned and bringing back Hydro-Man as a foe and a second time for the final story where a Spider-Man from another universe went insane from the events and bonded with the Carnage symbiote in an attempt to destroy reality. A version of the Clone Saga for the Marvel's Ultimate line, the Ultimate Clone Saga was also created. This one takes elements of the previous two, mostly the former.In 2009, Tom DeFalco and Howard Mackie—two people involved in the second Saga—reunited for a mini-series called Spider-Man: The Clone Saga, a "director's cut" and streamlined version of the story, with the supposed intent of telling the story as "originally intended". Some fans are crying Lying Creators, or at least, not-entirely-accurate creators since Life of Reilly indicates that many people intended the Clone Saga to be different things. The miniseries ends with Peter and MJ still married, and Ben, baby May, and Aunt May alive and well, though it does also use some ideas proposed for the ending of the Saga, such as Harry Osborn being the mastermind, albeit in an altered form than proposed.
Bond Villain Stupidity: The Jackal has Spider-Man at his mercy, but insists on wheeling his unconscious form across town and dumping him over the same bridge where Gwen died. In fairness, he's kinda nuts.
Breakout Character: Surprisingly enough, The Punisher's first appearance was a part of the storyline, being manipulated by the Jackal into thinking Spider-Man killed a minor character. He reappears in the nineties Clone Saga, this time visiting town for "Jackal hunting season."
Create Your Own Villain: The Jackal says as much, talking to a bust of Spider-Man before hurling it to the floor with a smash. Somewhat inverted, as Warren has only himself to blame.
Freak Out: In the midst of his budding romance with Mary Jane, poor Peter starts seeing a Gwen doppelganger roaming the streets of New York. This is, plainly, a scheme by the Jackal to drive his enemy completely batty. It works, too, with Peter reduced to hugging his knees and Hearing Voices when the clone turns up at his apartment.
Gollum Made Me Do It: Warren cannot reconcile his evil deeds and creates "The Jackal", a split personality who dresses like a deranged furry. He later manages to splice his human DNA with animal tissue samples, transforming into a bona fide Jackal (much like his earlier test subjects, which exhibited a Jekyll/Hyde alternation between man and beast).
He Knows Too Much: Warren goes mad after murdering his lab assistant, who walked in on him performing his initial cloning experiments.
Hypnotize the Princess: The Jackal can usurp control over Gwen's's mind if he wishes, although Gwen later manages to shake it off and call him a monster, which horrifies him. Played for Drama: the Jackal is a very sad, old man who sees himself as a hero.
Laser-Guided Amnesia: The Jackal uses a serum to alter the "RNA cells" (just go with it) that affect memory. This is why clones have no recollection of their deaths, or even being cloned in the first place.
Meet the New Boss: The Jackal's origin and M.O. is alarmingly similar to the late Green Goblin, almost as though he magically rose up to replace the clownish killer. He, too, suffers from multiple personality disorder and schizophrenia.
Mirror Match: Featured prominently on cover artwork, and eventually happens at the end.
Naked on Arrival: The Gwen Stacy clone, and later, all future clones who emerge from their pods. (The Jackal included.)
Red Herring: Poor Anthony Serba! Despite being drawn with a combover, a name hailing from Shiftystan, and a mug which wouldn't look out of place in Dick Tracy, he's not the culprit here. Far from stealing Warren's tissue samples for his own nefarious use, he tried to dispose of them right before Warren snapped and suffocated him to death.
Retcon: Even before the second Clone Saga, there were retcons of this story, partially because of an author-perceived Science Marches On. It was revealed that Miles Warren didn't make any clones, but infected people with a genetic virus that made them into copies. Then this retcon itself was retconned in the second Clone Saga when they decided to bring back the clone.
Armed with Canon: Peter trying on blond wigs in a department store with MJ and wondering how Ben thought it could possibly fool anyone. This was writer Howard Mackie’s dig at the notion that Ben could dye his hair blond to avoid identification. Adding salt in the wound, the “blond Ben Reilly” idea was pitched by the outgoing Editor-in-Chief, who was sacked in large part due to the inter-office chaos at the time.
When Ben Reilly criticizes Spider-Man's pact with Venom, he is speaking with writer Glenn Greenberg's voice. It illustrates the ideological differences between both heroes, but equally, the portrayal of Venom as an "anti-hero" left a bad taste in a lot of writers' mouths.
The Atoner: It was this era of Spider-Man's career that introduced Phil Urich, who attempted to re-purpose the Green Goblin costume and alias for justice.
Back for the Dead: Mendel Stromm, the Robot Master. Also Ben Reilly, thought to have been dumped into a smokestack and incinerated by a fearful Spider-Man.
Badass Longcoat: The first thing Nineties Jackal grabs after emerging from his cloning pod.
Biting-the-Hand Humor: Word of God says that the Bugle scenes contain several jabs at Marvel management for its handling of this storyline. In particular, Jameson has a run-in with businessman Roderick Kingsley at a gala; he offers (unsolicited) advice on how to reinvigorate the ailing newspaper: "Sell the majority of your shares to the public!" (Marvel tried that in 1991, leading to their bankruptcy five years later.)
Jameson: I'd never take the Bugle public, Kingsley—because I know that its long-term integrity would suffer under corporate connivers like you, who dream up ridiculous little 'schemes' which only produce short-term gains!
Averted at first but eventually played straight. The Clone Saga was filled with attempts to create Breakout Characters. None of them took off. On the other hand, the Clone Saga gave us What If? v2 #105, which gave us Spider-Girl.
Kaine is something of a break-out character introduced here, as he recently has gone on to have a his own solo series and joined the New Warriors. However he only took off after his return years later and not directly from the Clone Saga.
Civvie Spandex: Ben Reilly's Scarlet Spider costume involved a blue sleeveless hoodie on top of a standard spider-costume.
Clear My Name: Thank to Kaine screwing with Ben, Peter ends up getting blamed for Kaine's crimes (and has no alibi that could work without blowing his secret identity) and has to clear his name. Ben takes his place in jail while he does so. Kaine eventually relents and turns himself in after Peter threatens to reveal his identity in court to save Ben.
Comic Book Death: The nineties Clone Saga is rather notorious for it, given how it brought back not only the Peter and Gwen clones, but also Mendel Stromm, the Jackal, and Norman Osborne. Many of these characters are still with us; there's even a modest movement in the fandom to bring Ben Reilly back. There was a pitch to bring Harry Osborn back to life, as well.
The story sees Norman Osborn come back from the dead. Two people killed during the Clone Saga—Aunt May and Doctor Octopus—come back after the story's over.
Well, to be fair to Norman, he had actually been dead for more than 20 years in Real Life, so he arguably counts as a mild subversion.
Convenient Miscarriage: During the Clone Saga, Mary Jane was pregnant with Baby May. Baby May was originally supposed to tie into the storyline of Peter Parker not being the real Peter Parker. Since Peter wasn't the real Peter anymore, Marvel would have been able to get around the problem where having a baby would age Peter too much. But after the fan revolt, Marvel decided to make Peter the real Peter after all and the pregnancy storyline was dropped. It should be mentioned the writers implied Norman may have taken the baby somewhere; this was Left Hanging in the comics proper and is probably now Canon Discontinuity as of One More Day, but the Alternate Continuity comic Spider-Girl took the thread and ran with it.
Covers Always Lie: Many covers had blurbs teasing that new twists would be revealed, only for the issue to present no new developments. Also, during Maximum Clonage, almost every cover featured an army of Spider-Clones. They ended up only appearing for one full issue and a few pages, then dying with little relevance to the plot.
The Mark of Kaine was also said to be an amplified wall-crawling trait.
Specifically, using his wall-crawling/clinging powers to stick his hand to someone, and then rip it off, leaving a perfect hand-shaped mark. Of course, Peter Parker's "stick-em" powers are powerful enough to do the same, but most of his opponents only have their face exposed, so the results could be very gruesome.
Determinator: Peter is made to think his entire life is a lie. While he initially has a Freak Out, he comes to terms with it and moves on from there. Norman points this out:
"The death of Gwen Stacy, the revelation that your life was a lie, that you were a clone—through it all you found a way to not only survive, but to make a life for yourself. Through the worst of it, you prospered. And I HATE you for it!"
Discriminate and Switch/Mistaken for Racist: Ben Reilly as Spider-Man gets accused of being racist by an African-American man who turned out to be an undercover police detective, but the real reason Ben was suspicious of the man was because Ben's boss at the coffee bar he works at is the cop's ex-wife, merely said he was bad news and undependable, and was worried about their son being near him.
Both the Grim Hunter (Kraven's first son) and Doctor Octopus were killed early on in order to establish Kaine as a powerful threat. The former's creator Howard Mackie offered up the Hunter because he reportedly didn't know where to take him, and he has stayed dead. (Ock, however....
When the saga was reaching one of its intended wrap-up points, both the Jackal and Kaine, two major figures, were quickly killed off unceremoniously. Kaine got better, though, very quickly afterwards.
Once Peter was set to come back, several of Ben Reilly's villains were killed off in rapid succession.
Surprisingly averted with Ben Reilly, the source for a lot of hatred amongst fans. He was given a fairly respectful death at the hands of the Green Goblin.
Dye or Die: It's one thing to have two Spider-Men running around; it's quite another to have two Peter Parkers. So Ben Reilly goes blond. This also went a long way toward differentiating his character.
Expendable Clone: In Spider-Island, it's confirmed that the Jackal has a few squirreled away, leaving the nature of 90's-era Jackal uncertain. The current Jackal is a blend of old and new: He keeps the green fur and lupine anatomy of the original, but (like his clone counterpart) it's not a costume anymore. The version we see in this story has smaller ears and a full head of green hair.
Expy: The new Jackal is transparently patterned on The Joker in both look and temperament. He never stops cracking wise, and his death scene is a literal pratfall.
Fleeting Demographic Rule: The ultimate result, more or less. Suspicious test results, a Gwen Stacy clone still alive out there, somewhere...
Glenn Greenberg: The status quo, at least in that regard, is ABSOLUTELY NO DIFFERENT from the way it was in 1975 when the original clone story line ended.
A slight inversion in Norman Osborn, who was not resurrected only to be killed again. Instead, got promoted to the series' arch-manipulator and Villain with Good Publicity (as opposed to a lunatic Mad Bomber), as well as cementing his place as theArch-Enemy of Spider-Man. Over the next decade or so his threat hangs over Peter and his supporting cast and he ends up ruining many of their lives, or doing his damnest to at least.
Freak Out: Peter, when he starts thinking he's the clone.
Heroic BSOD: Spider-Man suffered two. The first one he's already in the middle of when the storyline opens because of his Aunt being in the hospital and his "parents" being revealed to be robots. The second is after Seward Trainer "reveals" that Ben in the real Peter and he's the clone.
Heroic Sacrifice: Ben gets in-between Peter and a goblin glider—taking a blade in the back and then falling to his death.
History Repeats: Ben is impaled and tumbles to the ground in a manner similar to Norman/Gwen. Also, he explicitly refers to himself as "Uncle Ben" as he dies.
Info Dump: See "Motive Rant." Glenn Greenberg was permitted to pen a one-off issue, The Osborn Journal, to tie up all of Norman's loose ends and explain why he'd been hiding in Europe all these years and masterminded the whole Saga.
The most obvious example of this was the climax of the saga which featured an evil army of Spider-Man clones. This part of the story was written aross different titles by different writers. One issue introduced the army in a Cliff Hanger panel. Another comic followed that up by having Kaine appear to help out, but being told not to kill any of the clones. The followup issue by yet another creative team depicted Kaine slaughtering several clones with no one objecting. The writer also didn't seem to know what to do with the army so he just had them randomly dissolve into dust with a brief line of dialogue about them being "unstable". In the end, the clone army had no real importance to the plot despite much hype to the contrary.
Leeroy Jenkins: The Scarlet Spider doesn't much cotton to Peter's longstanding truce with Venom.
Legacy Character: The people in charge were indecisive if Ben Reilly would become this or not. Ultimately he didn't.
A few were introduced for Kraven (The Grim Hunter), Doctor Octopus (Lady Octopus), and the Rose. The Grim Hunter got killed by Kaine, Lady Octopus only lasted a few years before the classic Doc Ock returned (though she later turned up in Spider-Girl), and The new Rose only lasted about as long as Lady Octopus.
Phil Urich became the fourth Green Goblin, but he was trying to be a hero. He got his own short-lived series, kicked around the main universe and became a recurring character in Spider-Girl.
The Man Behind the Man: The false DNA results for Peter Parker were fed to the Jackal by the Scrier Organization, who in turn were being led by Gaunt, who in fact was a Decoy Leader in the employ of the Scriers' true master, Norman Osborn. (He later rebranded the cult as The Order of the Goblin, a personal touch.)
Me's a Crowd: The objective behind the Jackal's "Carrion Bomb" is to turn the entire world's population into clones of Peter Parker. Not clones of the Jackal himself, or even a billion Gwen Stacys; just Peter Parker. As mentioned above, he's crazy, so it doesn't have to make sense.
Milestone Celebration: The saga was originally planned to end at Amazing Spider-Man #400, with Peter Put on a Bus and Ben becoming the new Spider-Man. Thanks to Executive Meddling, 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.
No Body Left Behind: A majority of the Jackal's clones collapse into goo once their number is up — even a copy of Gwen Stacy. Ben, conveniently enough, turns to dust. This allows Peter to give him a proper farewell by scattering his "brother's" ashes to the wind.
Opening a Can of Clones: The Spider-books in general are famous for this trope, but the 90's kicked it into high gear. Peter later uncovers the original clone's scorched remains in the chimney; probably the intention was to throw doubt on Ben's identity and put forward the possibility of both Spider-Men being clones. By this point, though, there were already so many clones running around, the effect was lost and the whole subplot was discarded.
Orcus on His Throne: Norman was introduced very late in the game, and didn't enter the picture until all of his subordinates were snuffed out. He later explained that he'd been living sumptuously in Europe and rubbing elbows with the Scriers, whom he ultimately usurped and converted into a tool for revenge.
Put on a Bus: Many of Spidey's old foes and supporting cast retired or otherwise let the titles to make way for Ben Reilly's foes and supporting characters, including Peter Parker himself. When Parker came back, so did everyone else. Meanwhile, Reilly's side characters vanished in a similar manner.
Red Herring: The Spider-Man skeleton left behind in the smokestack. It turned out to be the 'original' Ben Reilly, later replaced with a second clone by the Jackal; the new Ben mistakenly thinks he was alive for the original Clone Saga. (Confused yet?) It's pretty evident that the skeleton is a discarded escape route; you can tell the writers were getting desperate because hardly anyone even remembered the skeleton in the smokestack.
The Reveal: Norman Osborn is behind everything. Again, some consider it an Ass Pull, especially since even the writers didn't know who the mastermind would be, or even if there was a mastermind at first.
Roaring Rampage of Revenge: The whole saga is revealed to be Norman's revenge against Peter for Harry's death—which makes him responsible for everyone that got killed or hurt throughout. When this is revealed to Peter, Norman has also set in motion a plan to kill those in the supporting cast that he feels either wronged him personally or enabled Harry's death. And there's the question of Baby May...
Saved for the Sequel: The Gwen Stacy clone, who lingers on the periphery for another decade until Dan Slott nails her coffin nice and tight in Spider-Island (She returns for the sole purpose of getting whacked by her own personal Kaine, an aborted clone named Abby-L.) The Parker baby is also teased to have survived but, like the Gwen clone, this was born of the editors' desperation to keep sales up. Realistically, they had no way of knowing when or if these characters would turn up again, but they needed curious readers to keep following the books.
Seers: Kaine was one; according to Word of God, this ability was an amped-up version of Spider-Man's Spider-Sense.
Series Continuity Error: Spectacular Spider-Man saw Ben go after the Lizard during the events of Onslaught. However, Sensational, Amazing, and "Adjectiveless" Spider-Man saw Spider-Man get involved in the events of Onslaught, making them a Red Skies Crossover. Of course, this is not counting the retcons of the retcons of the first Clone Saga.
It should be noted that in the main Onslaught crossover miniseries, none of the two Spider-Men were ever present.
Also note that Spectacular was in the midst of a multi-part arc (centering on the Lizard). The first part was dated a month before the Onslaught crossover issues. Since said events are not referred to, the arc can simply be placed before those events.
Shoot the Shaggy Dog: It was fairly evident, even at an early stage, that Marvel was never going to allow Ben Reilly to replace Peter Parker in the mainline books. Nevertheless, the writers tried — wishful thinking, perhaps — to flesh him out with a new supporting cast, a new rogues gallery (mixed bag, that one), a couple of odd jobs outside the Daily Bugle, and a throwback personality akin to the Silver Age Spider-Man. There was even a 'Lost Tales' series dedicated to Ben's past adventures on the road. Very little of Ben survives in the canon, though his grumpy counterpart Kaine is still with us.
When the Saga returned in the 90's, The Punisher was brought in for the Maximum Clonage tie-in miniseries as a Shout Out to his first appearance in the original one.
The title Maximum Clonage itself being a shout out to the Maximum Carnage arc from a few year previous.
Split Personality Takeover: The Miles Warren personality looks to be well and truly gone: He emerges from his pod having undergone heavy genetic manipulation, effectively bringing his old costume to life. Inverted with Norman, who still possesses the cackling Goblin identity, but is equally monstrous outside of the suit.
Thanatos Gambit: With his dying breath, the Jackal says, "When the dream ends, the nightmare begins." This activates a hypnotic suggestion in Peter's mind, compelling him to try and murder MJ.
Took a Level in Jerkass: Norman, as exemplified by the mere fact that its him behind the whole thing in the first place, and not The Green Goblin. Years of Mind Rape against both Ben Reilly and Peter Parker are to be iced off with Osborn bombing every one of Peter's closest non-super friends, partly just for being that and partly because they pissed him off in various ways (regardless of whether they realised that or not), not to mention murdering(?) Peter and Mary Jane's unborn baby and presumably intending to take custody of his grandson Normie (his mum being one of his intended victims) and raising him in his own evil image after everything is over. He wasn't above killing anyone who got in his way in the process either. His very first act following his reawakening (fresh off the slab) is to kill a drifter of similar height and bury the body in his place.
Trailers Always Spoil: While the saga didn't have trailers per se, they did have a ton of advertisements and interviews with the creators, letting the public know the clone was coming back. During this time, there was a subplot involving a "mysterious drifter" with a connection to Peter Parker coming to New York who was obviously the clone. When the face of this character was revealed to be Peter Parker, there was a "tune in next time"-style blurb at the end of the issue as if it was supposed to be a big surprise.
The Unreveal: The end of the saga left fans wondering if Baby May was actually dead or had just been kidnapped. They were going to go with the former, but the writers were ordered to make it ambiguous (oddly by the very people that didn't want Spider-Man to have a child in the first place).
Villainous Breakdown: While explaining his plan and intentions to Peter, Norman maintains a rather collected demeanor and keeps his anger in check. When Peter keeps getting up during their fight, however, Norman becomes increasingly unhinged.
We Are as Mayflies: There's no telling how long clone denigration will take; like the mini-Jackal says, "It may take a few weeks — a few months — a few decades."
We Can Rule Together: The Jackal pitches this idea to Peter, who is already distraught over finding out that he's a clone. An ambiguous remark by the Jackal ("Couldn't have planned it better myself... or did I?") suggests, in hindsight, that he knew the test results were false.
West Coast Team: As Ben was being groomed to take the Spider-man mantle, Peter made preparations to transfer to another newspaper in Portland. The plan was for Peter, his journey now complete, to ride into the sunset with MJ and their new baby. Later, this was modified to Peter (still officially the clone by this point) self-exiling himself after his brainwashing in "Time Bomb", to protect his loved ones. Neither scenario took off.
Also, it was proposed that Ben have his own spin-off title. He ended up helming the Scarlet Spider books, but Marvel was in the midst of cancelling most of their spinoff books because they felt it was splitting the fanbase and costing them money.
Why Won't You Die?: After the part where Peter removes his and Norman's masks, Norman finally asks this.
Norman: I had you unconscious—at my mercy! How could this have happened? Why won't you just die?! Peter: Because then you would win. And I'll never give you that satisfaction.
Earlier Venom was beaten by Ben to establish Ben as a superhero in his own right. (In fairness to Ben, it look him considerable more effort to take down Venom than the few moments it took Kaine to snap the neck of a captive Doc Ock.)
Go Mad from the Revelation: The alternate Spider-Man was already steaming mad about the clone fiasco, but when proof that he might be the clone and not the Scarlet Spider emerged, he was driven over the edge and prepared to kill his counterpart.
Omnicidal Maniac: The end result of binding a murderous Spider-Man with the deranged Carnage symbiote.
Pragmatic Adaptation: Since Peter never got with Gwen Stacy in this continuity, it's Mary Jane who gets cloned.
Almost all of the clones and other characters are also written out as well, except for Ben Reilly who showed up for the interdimensional crossover.
Adaptation Distillation: It manages to wrap in most of the elements of the original in some form, as well as nods to other classic Spider-Man characters or stories along the way like the Scorpion and the idea that Peter's parents were alive, but it takes less than 10 issues and leaves very little hanging.
All There in the Manual: The identity of the disfigured clone that kidnaps MJ was confirmed to be Kaine in the Ultimate Secrets one-shot. The same one-shot confirms the six-armed clone to be Tarantula. Bendis on his message board stated the MJ-Goblin was Ultimate Demogoblin.
Composite Character: Ultimate Spider-Woman was given the name Jessica Drew ala the original version, her costume is based on the one wore by Julia Carpenter/Spider-Woman II/Arachne, and the red highlight stem from Ben Reilly's Scarlet Spider costume The latter is kinda fitting as this incarnation is basically a Gender Flipped version of Ben Reilly. Ultimate Kaine is wearing a messed-up version of Ben's Spider-Man costume. The MJ-Goblin creature is Ultimate Demogoblin.
While one of the clones is identified as Tarantula, his spider-like features and six arms bring to mind the "sort of" Spidey clone Doppelganger.
Adaptation Distillation: It tries to be, anyway. It removed a lot of the clutter and unnecessary (and unpopular) characters like Seward Trainor, Spidercide, Judas Traveller, Grim Hunter, and the Scriers at least.
Adapted Out: Several characters including Seward Trainor, Spidercide, Judas Traveller, Grim Hunter, and the Scriers were removed.
Alternate Continuity: Norman Osborn's still dead; Harry faked his death and is the mastermind; Dr. Octopus doesn't die, there's no Seward Trainer, Gaunt, or Spidercide; Ben Reilly meets his supporting cast during his Spidey tenure while he's still the Scarlet Spider; and outside of Harry getting locked up and the Norman clone dying, everyone lives happily ever after. Even the backstory was altered, having Aunt May's hospitalization changed from being a stroke to a virus and Peter not suffering a breakdown.
Came Back Wrong: The Norman clone wants to spare the baby and end the feud. Harry's believed the clone's defective himself, anyway.
The Gwen Stacy: Subverted. The Jackal tries to make a new clone, but he doesn't succeed and we don't see the original clone.
Heel Realization: Kaine realizes what Harry wants is wrong and delivers the baby back to MJ. Though probably defective, the Norman clone realizes Harry's mad and decided to end the feud and encourages Kaine's returning the baby.
Spared by the Adaptation: Ben Reilly and baby May survive the story. Granted, Doctor Octopus did come Back from the Dead and Aunt May was retconned into having been replaced and never having actually died, but they could count, too, since their returns were after "The Clone Saga" ended.
Take That: The Trade Paperback of the mini-series is called "The REAL Clone Saga"