A new six-part mini-series based on the outline of the original Clone Saga came out in September 2009. Written by Tom DeFalco and Howard Mackie, and drawn by Todd Nauck, this "writer's cut" mini-series will explore the story as it was originally conceived.
The first issue reintroduced Ben Reilly and Kaine, as well as addressed Mary-Jane's pregnancy and Aunt May's hospitalization, an infection that is seemingly uncurable. Ben and Peter bond after Kaine attacks them, and Ben stays in New York as Peter's blond haired cousin so he can build a life of his own. He also adopts the identity of the Scarlet Spider and works at the Daily Grind.
Ben, Peter, and Kaine reach the hideout of the shadowy figure responsible for infecting Aunt May and Mary Jane with a genetic virus. The villain is revealed to be Jackal, who captures all three and reveals that he plans to make an army of Spider-Clones to take over the world. Since Ben was the only clone to avoid degeneration, Jackal collects a sample of his blood to perfect his cloning technique, while noting that mixing blood samples of the two would be catastrophic. A mysterious figure watching the Jackal also wants to obtain this blood sample - specifically to be applied to the body of Norman Osborn.
Jackal explains that he intends to clone Gwen Stacy and another unknown figure - until Kaine breaks himself, Ben, and Peter free. During the subsequent fight, the clones desolve and Jackal suggests that Ben may be the original Peter Parker. Kaine kills Jackal, while Ben and Peter escape with the cure and save Aunt May and Mary Jane, who is later revealed to be pregnant. Peter retires, stating that Ben is the real Spider-Man, so Ben creates a new costume to go along with his reclaimed identity.
Peter and MJ begin planning for their baby while Peter also focuses on acquiring a research grant. Ben battles Doctor Octopus during a laboratory heist, who escapes after knocking down debris to distract Ben. After Ben tracks Octavius down, the villain notes that the newly costumed Spider-Man seems to be an imposter. Kaine arrives and attempts to kill Octopus (a departure from the original Saga, where Kaine actually murders Octavius, who is later replaced with a female Dr. Octopus) by asphyxiating him with some webbing and then flees. Ben shreads the webbing off, saving the life of his long-time enemy.
MJ's goes into labor while at the Daily Grind while she is having coffee with May, and after informing Peter and Ben they rush to the hospital. Donning web shooters, Ben and Peter swing to the hospital in their respective Spider-Man costumes (another deviation from the original story, the two never appeared in costume as Spider-Man together), coming into a short conflict with Kaine, who again flees, chased by Ben, as Peter continues to the hospital. At the hospital, nurse Allison Mongraine escorts everyone to the delivery room (Originally, Mongraine induced labor using poisoned coffee with a doctor's help, but in the new storyline, she is working alone). The baby is born and named May Parker. Mongraine takes the newborn out of the delivery room to clean her up, only to kidnap her and deliver the baby to Kaine at the docks (in a scene drawn almost exactly as it was in the orginal Saga). Kaine informs the shadowy mastermind that he has the baby, and is told in turn that it will be raised overseas.
The mastermind, now in control of a Parker blood sample, resurrects Norman Osborn, who is shocked by the identity of the man who has brought him to life. The mastermind, Harry Osborn, gives a Green Goblin mask to Norman and tells him that there is work to be done. Moments later, Ben (as Spider-man) is attacked by a new Green Goblin, who idenitifies Spider-Man both as "Ben" and a clone. The Goblin follows this by impaling Ben with his glider.
Ben is kept alive by the Goblin and captured as bait for Peter. After assaulting Ben, another man dressed as the Green Goblin reveals himself to be Harry Osborn and reasserts that Ben is just a clone. Kaine speaks with the revived Norman, who is also a clone, and discusses baby May's fate.
Kaine tells Norman that he feels baby May is his family in addition to Ben, Peter, Mary Jane, and the elder May, and she shouldn't be held accountable for the sins of her father. Harry activates a Goblin signal outside the warehouse (OsCorp), which attracts Peter, who is still searching for his daughter.
Peter enters the warehouse and finds Ben - only to be taunted by Harry - saying that he has decided to give the honor of killing Peter and Ben to Norman. Swayed by his conversation with Kaine - Norman blasts Harry with a Goblin weapon and tells him that he can't continue the cycle of violence; that Harry's madness is a product of Norman's sins. Peter frees Ben, and both help Norman fight Harry. Peter's shoulder is dislocated in the battle, and Ben demands to know where Harry has taken baby May. Meanwhile, Aunt May and Mary Jane wonder where Peter has disappeared to. Kaine enters the hospital room where May and MJ are through a window with baby May and gives her back to her family. May remarks that Kaine "seems familiar" and asks if they know one another. Kaine responds, "No, and that is my loss" and exits.
Back at OsCorp, Harry is restrained by Ben, so he activates his glider to impale Peter from behind. Ben prepares to leap in the path of the flying glider, but Norman jumps in the way, sacrificing himself to be impaled by the glider once more. Norman disintegrates due to cellular degeneration.
Harry vows to get even. The scene cuts to Aunt May, Mary Jane, Peter, Ben and the baby outside May's home (another depature, as the baby was missing at the conclusion of the original), where it is revealed that Kaine is missing and Harry is being held in a sanatorium. Ben leaves the city, but says he will return from time to time. Peter tells Ben that both villains were liars, and it doesn't matter who is the clone, but they each have a life.
The final page shows Ben riding away on his motorcycle and a giant mirage of the Scarlet Spider above him. In the distance MJ asks Peter if he thinks Ben will ever return and he remarks: "Trust me, MJ. We haven't seen the last of Ben Reilly-or the Scarlet Spider".
1) Updated diaologue (Ben mentioning American Idol, Jon Stewart, Tim Gunn, iTunes; Peter mentioning Cell Phones, Ben and Buzz mentioning the Internet. All of these things either didn't exsist, wasn't prominent or wasn't widely available during the original saga)
2) Spidercide, Traveller, The Host and Scrier are notably missing, among many villains who appeared during the original Clone Saga. (Stunner, Venom, female Doc Ock, Grim Hunter)
3) Drastically reduced supporting cast. (No Jessica, Jimmy Six, Seward Trainer)
3) Certain events happen out of sequence (Ben Working for The Daily Grind, dyeing his hair blonde while still The Scarlet Spider).
4) Kaine playing a larger role in the mini-series.
5) Ben actually meets Aunt May.
6) Norman is a clone, Harry is revealed as the mastermind.
7) Ben Survives.
8) Ben fights Doc Ock.
9) Doc Ock does not die.
10) The Daily Bugle is not shown in the whole mini-series.
11) Aunt May survives.
12) Peter and MJ keep the baby.
13) Neither Ben or Peter were confirmed to be the clone.
14) Ben does not join the New Warriors.