Peter was sitting on the couch in the living room of his house, as MJ was out, when suddenly a man in a Spider-Man costume broke in through the window. The costumed one web slung sharp and/or heavy objects at Peter, however he dodged them all before throwing him out the broken window through which he came in. When he looked out, however, he saw, to his horror, a whole army of Spider-Men outside. He quickly ran to his closet, put on the black costume, as he assumed that Ben was also under attack by clones and wanted to distinguish himself, opened the passageway, and swung out.
When he arrived at Ben's, sure enough, more Spider-Men were attacking. He swung in through the back window and tried to find Ben. When he did, he saw him in the Spider-Man suit trying to fend off the clones.
"There's too many of them, Ben." said Peter.
"What do you suppose we do about it?" said Ben.
"We need to figure out something that can stop them all." Suddenly Peter had a flash of memory of being in the Jackal's cloning lab and seeing a large device. He remembered seeing a label on it.
It said "Genetic transmitter."
"Of course!" said Peter, "The device in the lab, it's transmitting Peter Parker's DNA to the clones, it's what's keeping the clones from dying of no DNA. If we can deactivate it, they'll all die."
"That means one of us will also die." said Ben.
"Oh, yeah, well, I suppose if one of us must die to protect the other, especially considering the one who dies wasn't even supposed to exist, so be it."
Meanwhile, MJ was at a local restaurant and had just been served soup. She ate some but something was wrong. She, agonized, passed out.
Peter and Ben arrived at the Jackal's cloning lab and were trying to find a way to turn off the device, but they were attacked by two clones, one in a costume with the colors reversed on the body but with a normal Spider-Man mask and the other in a red costume with a black mask.
"You take gold eyes, Spidercide." said the red/black costumed one, "I'll take the other one."
"Right, Kaine." said the other. Kaine jumped Peter while Spidercide attacked Ben. The fight continued on, but eventually Spidercide and Kaine were knocked out, Kaine next to a large tube, but just as Peter and Ben began scoping out for a way to stop the machine, they were met by the Green Goblin.
"Harry?" said Peter.
"You're behind all this?" said Ben.
"You're quick," said the Goblin, "both of you."
"Ben," said Peter, "figure out a way to stop the machine, I'll take Harry." Ben went back to the machine.
"Why are you doing this?" said Peter.
"Stop pretending like you don't know. It doesn't matter to you why I'm killing you, anyway, or why I'm killing your daughter."
"What?" said Peter.
"Oh, haven't you heard?" said Goblin, "Your precious, pregnant MJ has been poisoned by one of my goons."
The scene cuts to MJ in the hospital with Harry voicing over.
"She's probably in the hospital right now. Not that she's going to be affected, but the baby sure will. She's likely in labor right now, working so hard to deliver that child. Imagine the look on her face when she learns the child was dead before she was even born!" While Harry was narrating MJ gave birth to a baby girl who appeared dead. The baby was then taken away by a nurse with red hair.
It cuts back to the lab.
"Damn you to hell, you monster." said Peter.
"I'm sure I will be, soon enough." said Harry, "But first, you shall die." He threw a pumpkin bomb at Peter, who quickly dodges. Peter jumped on Badbat. He punched Harry, but he had dodged. Harry pulled out a sword with a golden hilt and an obsidian blade carved in the shape of a bat's wing and slashed at Peter, but he dodged all the swings. After a while, Peter defeated Harry and turned him over to the police.
"Peter," said Ben, "I found out how to stop the machine."
"What is it?" said Peter.
"Remove the DNA sample being transmitted."
"Of course!" Peter grabbed onto one end of the DNA container's handle while Ben took the other.
"Goodbye, Ben." said Peter.
"Goodbye, Peter." said Ben. They both pulled the container out a little bit. Suddenly Ben experienced a moment of severe pain.
"So you were the clone all along." said Peter, "Harry must have tampered with the results." They continued pulling, but they eventually came to a point where Ben couldn't pull it any further. Luckily for Peter, it was out far enough that he could pull it out the rest of the way himself.
But before Peter could pull it out, Ben said "Take good care of my niece, Peter. Tell her about her Uncle Ben."
Peter didn't have the heart to tell Ben the truth about her death, so he just said "Okay." He pulled the DNA out of the machine, causing all the clones in the street to disintegrate. However, only one clone in sight did not disintegrate, Ben. Ben Reilly lay motionless against the wall, but it was obvious that he was still in one piece. Peter concluded that this was because he was the oldest clone and had the most time to develop a partial genetic code of his own. He picked up Ben's corpse and swung off.
Eventually, Spider-Man arrived at the cemetery. He dug a large hole next to Gwen's grave, in the spot on the opposite side of the one in which he asked to be buried when he died, and gently lowered Ben's corpse into the hole using webs. He then filled the hole, burying himself where he wanted to be, next to his lost love. He then swung home.
When Peter arrived home, he found MJ crying.
"MJ," said Peter, "Harry told me about what happened, with the baby and all."
"Harry did that?" said MJ, "Why would he ever want to hurt us?"
"Believe me, if I know, then Ultron is the greatest hero in the history of heroes."
The movie ends with Spider-Man swinging through the city with a narration by Peter.
"Saying my life is not an easy one would be the understatement of the millennium. My acting on responsibility has made enemies, sometimes out of my own friends. But one thing's for sure, no matter what life throws at me, I will take it, even if the whole world turns against me."
(Roll credits)
"So, would you prefer steel or vibranium?" said a man in a shadowy room.
"Vibranium," said another man in an undershirt, whose face is not shown, "I need them to be as strong as possible."
"Whatever you say, doctor."
"I swear upon your ashes, my master," whispered the man in the undershirt, "I will avenge your death, I will squash the Spider, vengeance will be mine." The camera pans to reveal the other man taking four metal tubes with appendages on the ends off a rack.
(Resume credits)
