The Sequel to Homecoming Spider-Man, and shows the connection between Amazing Spider-Man 2 and Homecoming Spider-Man.
Electro was exposed as a Skrull by the Real Electro (Crispin Glover) showing because of Agent Webb's (Marc Webb) greed, the only excuse was saying it was the Chameleon's (Alan Tudyk) idea because he wanted a skin Sample, and wanted to be the master of disguise so he allowed the Skrull to infiltrate the Spider-Dome. Meanwhile the clone (Andrew Garfield) realizes he was a clone and was betrayed by Dr. Miles Warren (Jemaine Clement) who reveals that he could never replicate the organic webbing but the Spider Sense which the Skrull wanted his sense, he was suppose to be the senator Ian Lang to replace the president, but disobeyed and did "A racial version of Black Lightning" which enraged the queen Veranke cause of his disobedience for his plan to overthrow the Super Skrull. After watching the footage an explosion hit and caused the clones to be destroyed and scaring the Clone who renamed himself Kaine, he hears a cry from an infant clone, in hopes to prevent the clone from being taken advantage of he places the infant into a orphanage only to be taken by Natasha Romanoff (Scarlett Johansen) revealing she was pretending to be Aunt May to "Toughen him up".
18 years passed after defeating Adrian Toombs, the clone (Tom Holland) who is disappointed in not being with Liz Allen, is hunting down the Chameleon who plans to infiltrate the bank. He stopped him only to realize he disguised himself as Liz Allen when his shape shifting powers starts to scramble. Now all of New York begin to realize he was behind the Vulture event and Tony Stark realized he was set up to look bad on Spider-Man only to have a punch in the face by Kaine who tells him "You had you chance to mentor him you swine, and you blew it". As the news broadcast was on, Kraven (Luke Evans) discovers his brother and unites with Electro to hunt him and Spider-Man down. Peter then asks the Chameleon why he tricked him, the only answer he got was revenge. He wanted to humiliate Spider-Man like he was long ago, he even revealed that Adrian Toombs was actually Reiner Drago and wanted to make him look bad at the Homecoming dance.
Chameleon was exposed by the media, Quinton Beck (Thomas Gibson), Alex O'Hirn (Ray Winstone), Adrian Toombs (Christopher Lloyd) whom was attacking Drago for stealing his identity, and Dr. Miles Warren who survived the explosion became the Jackal who plots revenge on Chameleon for his double cross, now brings up the plan to create "The Six". Enraged Peter then launches on Chameleon and while doing so he reveals that Osborne's been dead since he was the Green Goblin. He was toying with Spider-Man and the people of the dome, Ned joins in but gets shot in the leg by the Chameleon. Peter tries to apprehend the Chameleon only to be stopped by Kraven.
Elsewhere Miles Monroe was bitten by a spider, which was called the "Anansi Spider", then meets the actual Peter Parker (Matthew Broderick), he watches the media realizes his old foes are doing it again, then he returns to crime fighting realizes that he still has the same potential as he did 15 years ago after his retirement as Spider-Man. Nick Fury then realizes that Warren was cloning again, but was added by Black Widow pretending to be Aunt May, which hurts Peter after realizing Liz Allen wasn't the only person who was a fraud. the real Spider-Man realizes that the whole cloning thing was Black Widow's idea hoping to recreate the Spider Sense, this got the media to lose faith in their government.
Peter and the real Spider-Man escapes from a sixth member Carnage (Jenson Ackles), Mary Jane Watson (Jodi Benson) whom is married to Peter Parker explains to the clone that Aunt May passed away 15 years ago, the clone then feels humiliated on what an idiot Chameleon made him into. Peter explains that he was sure that Chameleon was apprehended and sent to prison, he watches the news that his math club knew all along that he was a clone and made the same mistake that agent Webb and Dr. Warren did (Trust the Chameleon), after this Peter trains the clone who is revealed can do organic webbing, Miles Monroe then joins in and decides to make a difference in the clones life to make amends for not being honest with him.
In a hideout in an abandon Hydra base in China Town, Kraven berates Chameleon for the stunt he pulled with not only the Skrull, but also betraying the Six to them since they now know about the cloning program, the Avengers, MRD, and especially the Six in a whole. Mysterio kicks the Chameleon out of the band for his betrayal and awards Carnage for his support, Mysterio reveals his plans to take over Smythe Industries and steal the Spider-Slayers and use them to hunt down the Spider-Man.
at the same time, Tony Stark realizes that he was set up to make him lose his patience and giving the Chameleon what he wanted Spider-Man's humiliation, after this revelation Chameleon was on a security footage revealing that he was Gustov Fiers, he planned the whole thing with the Skrull, Lizard, and all the events with the clone (Andrew Garfield), Stark then looks into when the Skrull was killed by the real Electro showing Stark as he was greeted by the Spider-Man that this was planned from the start, worse, that Black Widow was pretending to be both versions of May Parker. Thus Peter then was hurt then gets in a fight with Kaine who failed to keep him from S.H.I.E.L.D., but also failed to see the truth himself.
As they were going home, Kraven has Mary Jane by the throat and Carnage kills Michelle who is in secret a Hydra agent, the Spider-Men face off against Kraven and Carnage, Carnage reveals that Peter was polluted by the Symbiote long ago when Eddie was still alive, and that it got tired of Marvel's greed and stupidity taking bribes from the Skrulls, aliens that thrive on greed. They then kidnapped the group and brought them in front of a Amphitheater to execute Spider-Man, but when they arrived the Spider-Man on the stage was actually the Chameleon in disguise making the real ones look like impostors, but was killed by the Spider-Slayers controlled by Mysterio and Electro the people see that it was the Chameleon and blamed themselves for believing him, Mysterio then states that they have no one to blame but themselves revealing they were the real villains, because of their ungratefulness, excuses to hate, choosing to blame others for what wasn't actually their fault.
After his speech he then raises a sword to stab Spider-Man, but Electro stopped because he understands why he did what he did and states "But Skrulls I hate MORE", Electro realizes that Carnage was the true mastermind and tries to kill him, but Iron Man stops him as a way of making things right with Spider-Man, he fights Mysterio. The other Avengers came to help such as Captain America battles Kraven, Hulk battles Rhino, Thor battles Electro, Vulture battles Vision, Black Widow shoots Nick Fury whom been helping Spider-Man from the beginning, realizes her betrayal only to see Black Widow killed by Carnage who exposes her as the Queen Skrull herself Veranke. This reveals the Chitauri was a distraction while the Skrulls were the real invaders as they cry out of the death of their queen, the five members were defeated, but Carnage rams into Spider-Man hoping to kill him, but notices that Beck lost control over the Slayers and they are on a rampage, Peter kicks Carnage into the slayer not before Kaine jumping in front of Carnage's web, thus both died in the slayers explosion, which was Ironic because Eddie died the same death.
After the incident Peter Parker renames the clone "Ben Riley Parker" in honor of his late uncle, The Avengers accepted Peter as Black Widow's replacement and studying the Skrulls language to see if more were out there. The Sinsister Five members were seen in The Raft, a prison for Terrorist organizations, Electro serves as the power source to help him and gets visits from his wife and son, Kraven mourns the death of Chameleon even though he betrayed them, Vulture retires in a retirement home making Drago (Michael Keaton) his official successor, Rhino confesses that he cause the Gamma explosion under Ross's orders so Banner can be blamed, which gets Ross fired from being Secretary and arrested by the law. Mysterio plotting to try it again making plans for the future, the story ends with Peter, Ben, and Miles using their Spider abilites to patrol the city.
After the first credits, Dr. Miles Warren in hiding realizes that he shouldn't trust Chameleon, he is seen recreating Kaine, along with a symbiote known as Toxin for phase 4 for the Cloning program.
Tom Holland - Peter Parker Clone/ Ben Riley/ Scarlet Spider: he realizes he was a clone and a pawn to Chameleon's scheme of revenge, in the end he becomes the Scarlet Spider.
Andrew Garfield - Kaine Parker: the first clone in the attempt to recreate the Spider-Sense, when the Skrull attacked in Amazing Spider-Man 2, he is seen with a scar on his right eye, and wears what use to be Harry's Goblin armor from Spider-Man 3.
Matthew Broderick - Peter Parker/ Spider-Man: a retired hero who settled with Mary Jane Watson after the events of Spider-Man 3, he becomes the clones's mentor and father to teach them how to use their powers, in the end becomes the leader of the avengers after Iron Man steps down.
Thomas Gibson - Quinton Beck/ Mysterio: unlike his comic counterpart, he was a former S.H.I.E.L.D. agent who was betrayed by Black Widow during the Skrull crisis, he stole Dr. Strange's eye stones and uses them to see through the orb around his head, he actually wears the original Green Goblin Armor.
Robert Downey Jr. - Tony Stark/Iron Man: Billionaire who seeks redemption from Spider-Man for falling for Chameleon's scheme.
Luke Evans -Vladimir "Kraven" Kravenoff: a skilled hunter hired by Beck to kill Spider-Man, but also gets caught up in a family affair to teach Chameleon a lesson for his stunt with the Skrull in Amazing Spider-Man 2.
Khary Payton - Miles Monroe/ Black Spider: based on the Spider-Man from the Ultimate universe, helps Spider-Man with the enemy the Sinister Six.
Jodi Benson - Mary Jane Watson: retired from acting she is a mother of Mayday Parker, she is shown to have remorse for her past action in Spider-Man 3, and is shown to be more maternal to the clones.
Crispin Glover - Maxwell Dillon/ Electro: based on the original Electro and hates Skrulls more than Spider-Man after one stole his identity and tortured them just to infiltrate the dome. Glover states that he will have similar screams as Grendel when he shoots electricity because it hurts him making his bones a conductor.