Part 3 deals with the events that occurred between the time that Ben Reilly took the guise of Spider-Man and the end of the entire clone saga. The clone saga concluded with the storyline Revelations and the Mastermind of the whole saga was revealed. Spider-Man and Peter Parker's life would never be the same again!

Key:

ASM = Amazing Spider-Man
SPEC = Spectacular Spider-Man
WOS = Web Of Spider-Man
SPID = Spider-Man
SEN = Sensational Spider-Man

Ben now as the new Spider-Man battles the Scorcher, a villain from Spider-Man's past as told in the series Untold Tales Of Spider-Man.

Spider-Ben battles Tombstone with help from the Punisher.

Peter and Mary Jane move to Portland where he goes to work at the company, Galannan, that sponsored the exhibit where he gained his spider-powers when he was bit by a radio-active spider...He ends up battling a villain by the name of Tendril and Dryrot and he eventually loses his powers...Ben makes an appearance in the final two issues where he talks with Mary Jane after she came back to New York for awhile.

A flashback story taking place right after the events on Sensational Spider-Man #0 involving Kraven the Hunter and various supporting cast members at the time (roughly after Amazing Spider-Man #56). Ben battles thugs on a train.

Ben meets the Human Torch and battles the Sandman without the knowledge at the time that Sandman is on the good side of the law.

Ben battles El Toro Negro and Poison

Ben battles a new character named DK who is somewhat of a muck-monster like Man-Thing.

Ben battles Skull-Jacket along with the Black cat.

Ben and Venom have a battle royal in this 4 issue limited series.

Media Blizzard

Ben fights Mysterio and Armada in a 3 parter.

The Return Of Kaine

Kaine returns from a regeneration pod at the same time a skeleton with a torn up Spider-Man costume is retrieved from the smokestack in the incinerating plant where Spider-Man left the clone's body years ago & it becomes a major news item...Kaine meets Ben again after battling the Rhino then a major brawl breaks out with Ben, Kaine, The Rhino, Polestar & Joystick...Kaine eventually vanishes yet again then Spider-Man returns from Portland with Mary Jane to see what the skeleton represents.

Ben battles Superboy and defeats him in one of the 2-universe big battles and meets the Joker from the DC Universe...Peter Parker meets Clark Kent and Lois Lane at the Daily Planet where J. Jonah Jameson also works...In a cameo appearance, Spider-Ben fights Man-Bat.

Ben & The Silver Surfer battle a Mad Thinker Robot then Quasimodo and even Thanos.

Ben meets Spider-Man and Mary Jane again after they have arrived back from Portland after a battle with the new Doctor Octopus.

Web Of Carnage

Ben discovers that the women that he met in Sensational Spider-Man #0, Jessica Carradine, is non other than the daughter of the burglar that murdered Uncle Ben way way back in Amazing Fantasy #15. And if that's not the least of his problems, the skeleton discovered from the smokestack is revealed to be another clone of Peter Parker...Ben goes on to become Spider-Carnage as the Carnage symbiote takes control over Ben.

Ben helps the New Warriors battle the villain Advent, this time as Spider-Man.

Blood Brothers

Jessica Carradine discovers that Ben is Spider-Man and displays her hate for him as well...A new mysterious character is introduced and he seems like he is on life support. He is named Gaunt. The Daily Grind coffee shop is destroyed by fire...As Ben goes on to battle the Hobgoblin, Osborn Industries is revealed to be financing Multivex, a research company involved heavily in the clone saga...The Molten Man gets involved in the mix and battle both Ben, Spider-Man, and then Gaunt...Multivex explodes after all the battles.

Ben battles the Beetle, Shocker, Jack O' Lantern, Scorpia, Boomerang, and the Pro. The skeleton is handed over to the authorities.

Ben makes only a cameo appearance as Spider-Man again. His last appearance in New Warriors.

Ben makes only a short appearance in the Daily Grind coffee shop as they get a new customer: Eddie Brock!

Ben battles the Hobgoblin once again as Peter and Mary Jane receives a welcome home party.

Ben goes up against Will-O-The-Wisp and his creator Jonas Harrow.

Ben and the Fantastic Four team-up and journey to another world.

Ben meets Daredevil and fights the Shooter.

Jessica Carradine realizes that Spider-Man is truly a hero after Ben saves the life of a child.

Ben fights Mysterio and Armada.

Ben begins a battle against the mob.

Ben continues his fight with Jonas Harrow and Dragon Man joins the battle.

The 4th Green Goblin, a hero, fights an illusion of Spider-Man (Ben) created by the villain Arcade who is hired by Gaunt to kill the Green Goblin.

Ben makes a cameo appearance.

Nothing major happens in this issue.

Ben battles a new Villainess named Delilah and a new Rose is introduced.

Ben goes up against Hammerhead as his battle with the mob intensifies.

Peter regains his Spider Powers that he lost during the Final Adventure limited series & Ben begins a fight with the Lizard.

Ben versus the Scorpion with a little help from Powerman and Iron Fist.

It's Ben against the Looter. The first time since the Cyberwar storyline begun in Web Of Scarlet Spider #2.

Ben tries his best against the extremely powerful X-Men mutant killers the Sentinels.

Ben continues his fight with The Lizard.

Ben and The Avengers battle the Spider-Man robot created by Kang from Avengers #11 way back when.

Ben begins a battle with Swarm.

In the middle of the Onslaught War that rushed many Marvel heroes to another world, The villain Gaunt meets with Scrier and many mysteries are soon to be revealed.

Ben takes on Tombstone.

Ben's fight with the Lizard concludes.

Ben concludes his fight with Swarm.

Mysteries start to unfold as Traveller is revealed to be a sham. He possesses only limited Psionic powers and the ability to alters other's perceptions of reality. Scrier is discovered to be an organization rather than an individual. Peter and Ben battle the Scriers to try and help Traveller and Peter dons the Spider-Man attire once again. In the end Traveller escapes Scrier as Scrier's employer and Mastermind behind the clone saga wants him dead...Gaunt kills the individual Scrier we got to know for this failure.

Ben and Daredevil fight HYDRA.

Ben makes a 3 page appearance fighting street thugs.

Ben and Ghost Rider battle the Wendigo.

A woman by the name of Janine from The Lost Years limited Series, comes back to visit Ben and they fall in love but Kaine is responsible for luring her back as "bait". We learn that Kaine's suit is designed to slow down his physical degeneration...Ben and Kaine fight once again and Janine turns herself over to the authorities for killing her father years ago after she was abused by him. Kaine follows suit and also turns himself over to the police.

Ben makes a minor couple page appearance along with some of the X-Men.

Ben and Gambit battle Tombstone in the first story then he teams up with Howard The Duck to fight the Circus of Crime.

Ben battles Cardiac, Joystick, and El Toro Negro. 

Revelations

After years of the clone saga, the Mastermind behind the whole thing is revealed. Slowly but surely we learn more and more about the man who is in the background all this time...Seward Trainer is forced by Gaunt to rejuvenate him the Gaunt takes his new robot form. Trainer is killed by the Mastermind...Gaunt goes on to battle Ben and is revealed to be Mendell Stromm, Norman Osborn's ex partner who was thought to be dead after a heart attack. A woman named Alison Mongrain begins work at the Daily Grind. She drugs Mary Jane's soup...Mary Jane goes into labor and sadly loses the baby as Gaunt continues his fight with Ben who is now joined by Spider-Man...Gaunt is defeated and killed for his failure by the Mastermind who is shockingly revealed to be Norman Osborn, thought dead for many years. Mongrain delivers a package to Osborn who many think to be Peter and Mary Jane's baby...The return of Norman Osborn can only mean the return of the original Green Goblin and he does indeed return with a major battle with Spider-Man. Peter/ Spider-Man is revealed to be the true Peter Parker and sadly, Ben dies from being impaled by the goblin's glider (very similar to how Norman "died" in Amazing Spider-Man #122) trying to save Spider-Man...Spider-Man is finally convinced he is the true Peter Parker as he watches Ben disintegrate before him.

The Clone Saga Concludes!