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.
Spider-Man: The Clone Saga (2009) includes examples of the following tropes:
- Adaptation Distillation: It simplifies the story and removes 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: Harry believes this to be the case with the Norman clone, who ended up a Morally Superior Copy who wants to spare the baby and end the feud before anyone else gets hurt.
- Civvie Spandex: The Scarlet Spider once again wearing a hoodie as part of his costume.
- Clone Degeneration: Kaine again, though Jackal does try to find a serum to cure it and Dr. Octopus later completes it.
- Clone Angst: Again, it is a version of the Clone Saga, so this is expected between Ben and Kaine, who like in the original, lament their status as clones. Averted with the Norman clone, whose lamentations revolve around the person the original Norman's actions turned Harry into.
- Compressed Adaptation: While the original was going to span six months and ended up spanning a few years, it was also planned to span across four titles. Here, it tries to cram all of it into six issues of a single series.
- Death by Adaptation: Norman Osborn is still dead in this version.
- Evil Knockoff: Kaine is an evil clone of Spider-Man.
- Faking the Dead: In this version of events, Harry does this so he could prepare for his plans here.
- Heel Realization: Kaine realizes what Harry wants is wrong and delivers the baby back to MJ. The Norman clone also realizes Harry's mad and decided to end the feud, encouraging Kaine's returning the baby.
- Heroic Sacrifice: The Norman clone leaps between Peter and the Goblin Glider, similar to how Ben in the '90s story did, to save Peter's life — and thus die the same way the original Norman did.
- Morally Superior Copy: The Norman clone ends up being this to the original Osborn, horrified by the monster the original's actions warped Harry into being and doing everything he can to stop Harry, even performing a Heroic Sacrifice to save Peter.
- Mythology Gag: How the Norman clone dies, taking the blades of the Goblin Glider intended for Peter, both to the '90s story ended with Ben dying to save Peter and —though the context is different — how Norman died in The Night Gwen Stacy Died, doubling as a Call-Back to that story.
- Series Fauxnale: The mini-series works as an open-ended one for the Spider-Man saga. The Osborn/Parker feud is resolved, at least for now, with Harry incarcerated, Aunt May is still alive, and Peter and Mary Jane are parents with Peter presumably semi-retired, and Ben opts to leave New York behind and resume life on the road. There is room for new stories down the road should Marvel choose to tell them.
- 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!: When first announced, fans believed the series would take the place of the 1990s Clone Saga and explain how things went down in the wake of the revised history brought about by One More Day with Peter and MJ unmarried. What they got instead was a series that honoured the Spider-Marriage and provided many a jaded reader with a happy ending for the Parkers and a potential jumping-off point if they were no longer satisfied with the direction of the main book, which would carry onward with an unmarried Peter.
- The Trade Paperback of the mini-series is called "The REAL Clone Saga"
- In the last issue, Harry refers to his battles with Spider-Man as being like an addictive dance, describing the sensation as being "like the Macarena, only cool."
- Taking the Bullet: This time, it's a clone of Norman who takes the Goblin Glider for Peter.
