Meanwhile, Kaine lets Peter know that he feels no guilt for letting Ben Reilly take the blame for the murder, no matter what name he goes by. Kaine and Spider-Man battle it out to try and settle this once and for all. Though Kaine is way more powerful than him, Spidey does not give up.

Elsewhere, Detective Raven and Stunner catch wind of a report about Spider-Man and Kaine fighting each other. They head over to the scene of the battle to try and capture Kaine, whom they also believe to hold the key to prove Peter Parker's innocence. While this takes place, the battle rages on between Spider-Man and Kaine. Spidey garners all his strength to try and stop Kaine. He has no idea what happened between Kaine and Ben to cause Kaine to hate Ben so much. Nonetheless, Spidey vows to bring Kaine to justice and set Ben free.

Detective Raven and Stunner arrive on the scene of the Spider-Man/Kaine battle. Stunner prepares to jump in the mêlée but before she or Raven can do anything, Judas Traveller appears and teleports both Kaine and Spidey away from the area.

In Amazing Spider-Man #403, Part Two of the Trial of Peter Parker storyline, while Ben Reilly impersonates Peter Parker, who is on trial for murder, Spider-Man faces a trial of his own. His trial is presided over by Judas Traveller, while Carnage handles the prosecution and Kaine, John Jameson and Dr. Kafka are in charge of his defence. The jury is made up of Ravencroft inmates. The objective of the trial is to determine if Spider-Man, by his very existence, is responsible for the creation of these super-villains and to determine if his death would somehow "cure" them. Infuriated, Kaine attacks Traveller, calling him "Scrier's Man". Though unfazed by Kaine’s attack, Traveller does not accept being called that.

Meanwhile, at the trial of Peter Parker, Mary Jane is on the witness stand. The prosecution bombards her with questions about Peter's frequent absence and asks her where he was a few years ago when he went missing and no one knew where he was. MJ knows where he was – he was buried alive by Kraven the Hunter – but she cannot tell them, as it would reveal that he lives a double life as Spider-Man.

Back at Spider-Man's trial, Carnage blames Spider-Man for his existence because it was Spider-Man that brought the symbiote that transformed Cletus Kasady to Earth. Kaine cross-examines Carnage by attacking him. They battle it out for a while until Traveller puts an end to it. Spidey starts to feel that, though Kaine has committed anis crimes, there seems to be something beneath the darkness that surrounds him. Carnage's next witness is Malcolm McBride, also know as Carrion. Carnage asks McBride why he experimented with Professor Warren's Carrion virus in the first place. Before McBride can answer, Carnage suggests that perhaps he was jealous of the success of another of Warren's pupil and, as such, he became irrational and started experimenting with the virus. Carnage asks who the student was, to which McBride replies that his name was "Peter Parker". With that, Carnage moves towards Spider-Man and unmasks him, revealing that Spider-Man and Peter Parker are on and the same. He then claims that, no matter what his identity is, he destroys everything and everyone close to him.

Furious that his identity is once again compromised, Spidey breaks free of his shackles and confronts Traveller. Spidey offers to give himself up to Traveller, as long as he is allow to bring Kaine to justice first so as to clear Peter Parker's name and save Ben Reilly's life. Traveller completely ignores his plea and asks the jury for their verdict, even before allowing the defence to present their case. The verdict is immediately returned and Spidey is found guilty. As such, Traveller sentences him to death, which is to be carried out by the prosecution and jury, which consists of other super-villains.

Things go from bad to worse when Spidey is paralysed by Traveller. Fortunately for him, Kaine comes to his rescue and engages into battle with the super-villains that are trying to kill him. Kaine battles them admirably and fiercely but they are too much to handle alone. Strangely, Traveller chooses to end the battle by teleporting all of the villains back to their cells before they kill Kaine. Spider-Man asks why he came to Kaine's aid and Traveller reveals that he did so because he needed to understand him. He explains that the fact that a corrupt soul like Kaine would sacrifice himself for him speaks more about Spider-Man’s life than his actions ever could. Traveller then concludes that his experiment is over and teleports Spider-Man and Kaine back to where they were last. As they reappear over there, Stunner is waiting for them.

Back at the Ravencroft Institute, Carnage is in his cell, planning to kill Peter Parker and his family. Traveller visits him and wipes all of his memories, claiming that the knowledge of Spider-Man's secret identity is too precious for him. He does the same to all the other villains who witnessed the day’s events.

In Spider-Man Volume 1 #60, Part Three of the Trial of Peter Parker storyline, the story opens up with Stunner attacking Kaine and Spider-Man. She gets the upper hand against a weakened Kaine but Spider-Man comes to his rescue. Their battle is so violent that it causes a nearby building to collapse, nearly killing them. Pulling herself out of the wreckage, Stunner disappears. Spider-Man also extracts himself and Kaine from the rubble and tells Kaine that he (Kaine) is coming to the trial with him. Kaine replies that he will fight him with every ounce of strength he has to keep him from helping Ben Reilly, who is impersonating Peter Parker, while Peter tries to sort things out, which is what he is doing right now. Spider-Man understands where Kaine is coming from and nods in understanding. He then proceeds to put all of his power into a single devastating punch that knocks him unconscious.

Spider-Man is in the process of dragging Kaine into the courtroom when Kaine breaks free and attacks him. The battle is again quite violent, as both men throw each other through walls and create enough of a disturbance to cause the judge presiding over the Parker trial to call for a recess. The fight spills out into a private room where Kaine tells Spider-Man that they need to stop fighting. Spidey agrees as long as Kaine tells him the truth about everything. Kaine explains that if he – Spidey – would examine his actions, he would understand that Kaine is only trying to protect Peter Parker and that he just cannot allow him – Spidey – to throw it away and risk everything for Ben Reilly. Having said that, and wanting to prove his point even more, Kaine removes his mask and his face, though scarred, is revealed to be that of Peter Parker. Kaine reveals that he was the first clone of Peter Parker created by Professor Warren and that the degeneration factor has started to take effect, preventing him from ever having a real life. He goes on explaining that the degeneration factor also had an effect on his powers, somehow increasing them and making him more powerful than both he and Ben. He then explains that all of the above reasons is why he spend most of his life making sure that Peter Parker's life would never be in danger.

Spidey understands where Kaine is coming from but still cannot believe that he would not help Ben Reilly. Running out of options, Spidey realizes that the only way to save both Ben and clear his name is to reveal his identity to the world and explain everything about the whole clone saga (a feat, not the least). Kaine begs him not to do it but Spidey ignores him and enters the court to offer new evidence that will prove Peter Parker's innocence. He starts to pull his mask off when Kaine interrupts him and approaches the judge's bench to come clean. Kaine tells the judge and the whole court that he has hated Peter Parker ever since Parker took a picture of him while committing a murder and that, to get his revenge on him, he altered his fingerprints to match his, so as to implicate him in his most recent murders. Having said that, Kaine lets the court take his fingerprints as evidence to support his claims. Kaine will not go down that easy however and he sets out to do what he has wanted to do for years, which is to carry out Ben Reilly's execution. At issue's end, he lunges himself at Ben, who is in fact impersonating Peter Parker, which is a fact that Kaine does not seem to know...yet.

Minutes later, the news of Peter's exoneration reaches the newsroom of the Daily Bugle where all in attendance shout their approval. Even J. Jonah Jameson is ecstatic, though he prefers to express his excitement in the confine of his office.

Meanwhile, miles away, the Jackal is questioned by yet another clone of Peter Parker about when he will be allowed to destroy the Parkers and Ben Reilly. The Jackal advises him to be patient and he then promises him that, as soon as he's finished making the necessary adjustment to the Carrion virus, they will have a "family reunion".

Kaine is making a formal confession to the authorities. He explains how he easily killed Doctor Octopus and how he murdered Louise Kennedy, Detective Raven's late partner. Standing outside the interrogation room, Detective Raven suddenly realizes he has been holding his breath. For the past three years, he has relentlessly pursued the man who murdered his partner. Three years...and all that he has sacrificed comes down to three simple words "I killed her".

Alone in his private laboratory, Dr. Seward Trainer checks and rechecks the results of the genetic tests which he recently ran on the Parker foetus (as shown in Web of Spider-Man #124). What he discovers is astounding and hopes that Ben Reilly and Mary Jane are prepared for a shock.

Peter, Ben and Mary Jane reunite at the Parker home where they get a phone call from Seward Trainer asking them to come down to his laboratory immediately.

Kaine is being brought over to Ryker's Island when he gets a vision of Mary Jane dead. This time however, her murderer lurks in the shadows and to Kaine's surprise, something about this mysterious figure strikes a familiar chord. Kaine wonders who the mysterious individual is.

Seward Trainer gives Mary Jane the wonderful news that her child appears to be very healthy. However, something else that he has discovered troubles him. When running tests on the foetus at the genetic level, he detected some kind of genetic drift, which caused the anomaly that first brought Mary Jane there. And he has come to only one conclusion that could explain why that is: one of the parents is quite possibly a clone. Totally enraged, Peter accuses Trainer and Reilly of trying to screw him over and, grabbing Mary Jane, he prepares to leave. MJ implores him not to leave until they finally learn the truth. Peter argues that Trainer and Reilly are plotting against him but MJ convinces him to do the tests himself to make sure they do not try to sabotage it. Seward Trainer jumps in the conversation and explains that he has not vested interest in the final outcome and even offers that they use his equipment to perform DNA tests on themselves and compare results. Peter reluctantly agrees.

And so it begins. Blood and tissue samples are taken, scrutinized, compared, contrasted, analyzed and subjected to an exhausting variety of examinations. Mary Jane watches on and she does not even attempt to disguise the fear that lurks within them. She desperately wants the burden of uncertainty forever lifted from her husband's shoulder. Once again, Peter Parker is on trial for his life and the lives of those he loves. And this time, a final verdict must be reached and rendered without prejudice or any hope of appeal. After what seems to be hours, Ben and Peter reach the same conclusion. Peter is the clone and Ben Reilly is the real Peter Parker. Totally infuriated, Peter lunges at Ben, accusing him of trying to steal his life. As they fight, Ben argues that Peter should never have had it in the first place and that he is the victim of all this. As the battle rages on, Peter accuses Ben (and Trainer) of playing him just like Kaine and the Jackal have done over the past months. Peter then grabs Ben in a chokehold and, as he starts to strangle him, he yells at him that he will make him confess even if he has to choke it out of him. MJ, who is being held back by Seward Trainer, who fears that she will get hurt, rushes over to Peter to try and reason with him. In a blind rage, Peter backhands her and sends her flying across the room and into a wall. When he realizes what he's just done, and how far he's gone over the edge, he takes off, totally ashamed about what he just did. As MJ lies on the ground with a bloody nose, she begs Peter not to leave, but to no avail.

Elsewhere, the Jackal is now ready to begin mass-producing his new and improved Carrion virus. But before doing so, he needs a certain isotope, which can be found in the Genetech Research Complex in Sayville, Long Island. Handing the Parker clone a costume he designed for him, the Jackal sends him on his way and tells him that "the day will come when clones like him rule the Earth".