(from my perspective, of course)
Let's start from
In Civil War, after Peter has a few quick appearances stopping street crime, we find out that Tony has files on Parker's identity (This could be where we get a quick summary of Peter's origin from Stark, as he shows his knowledge on Peter's life). He blackmails Peter into joining his cause, threatening to out him to the public. Peter reluctantly joins, but after realizing the things he would have to do as a Pro-Reg hero, he eventually decides to defect to Cap's side. He successfully hacks into Tony's files and deletes all evidence, and then steals some equipment. However, Iron Man detects his plan and flies to stop him. Peter trashes his suit and webs Tony to a wall, while Tony calls in backup. After this, Tony builds his Bleeding Edge armor. Spidey decides to flee, knowing he can't successfully face multiple superheroes.
After joining Cap, he uses his intellect to help their side. He upgrades their tech while constantly coming and going (to school, home, etc - we should know where he goes but not see where he goes). Also, he begins to works on a project for himself. In the final battle, he takes on Iron Man, revealing the secret project - the Iron Spider suit (If he says he didn't have time to change the paintjob that would be a good quip).
Spidey's suit is more powerful, but he has less experience so they have a good fight. It ends with Tony's Bleeding Edge armor being destroyed, injuring civilians all over. Spidey realizes what has happened and rushes away to save as many bystanders as possible, kicking himself for being irresponsible. Now that Iron Man doesn't have his best armor, he summons an older model to help him as Cap attacks. This is when Cap vs. Iron Man happens, causing more collateral damage which Spidey desperately tries to mitigate and save as many civilians as possible. Slowly, the other heroes follow Spidey's lead, until only Cap and Iron Man are fighting. Then, one of Cap's mighty blows is dodged by Iron Man and heads for a civilian. Spidey saves the civilian, but his suit has taken too much damage and finally breaks down. Cap realizes his errors and stands down. The war ends with the Pro-Reg side winning, but granting a temporary amnesty to the Anti-Reg heroes. This is one of the reasons why the public is against Spidey - as he is against the the law, technically. As a huge fan of Iron Man, Spidey's victory against him really angers J. Jonah Jameson and pushes him into starting a slander campaign against Spidey.
After the movie is done, we could see Peter checking his voicemail with TONS of messages from an angry and worried Aunt May.
SIDE NOTE - The plot is based off this leak
The movie starts off in Midtown High, as star student Peter Parker pushes his way out of a locker. He gets hit on the head by a basketball thrown by Flash Thompson - the school bully. Flash and his buddies are watching a Spidey video on their phones - Peter tries to step in and join the conversation but is pushed away. Fellow science nerd Gwen Stacy (and his only friend) says hi and they begin a conversation. She doesn't know that he's Spider-Man. Meanwhile, an impostor Spider-Man is robbing banks all around town, ruining Spidey's bad reputation even further. Peter gets a ping on his smartphone and ditches class to stop the crime. The impostor is good, but doesn't have superpowers and is defeated fairly easily. Spidey webs him up and unmasks him when he is suddenly gassed by the mask. Spidey, hallucinating, starts rampaging around the city - throwing cars and destroying buildings, etc. A Pro-Reg member comes to stop him and they fight. Eventually, Spidey manages to throw off the effects of the gas and comes victorious over the other hero, webbing him up and returning to school. The teacher is angry - he asks why Peter rarely shows up to class and never hands in any assignments and yet gets perfect on all the tests. After school, Gwen says that she signed Peter and her up for a science fair competition - the top prize is a lot of money, a scholarship to ESU and an internship at a new competitor to Stark Industries: Horizon Labs.
They are working against each other but Gwen decided to sign Peter up as they are good friends (shows how close they are). Peter goes home to think of ideas, and starts working on a tracker object. The next evening, there is another Spider-Man robbery taking place. Spidey gets there, but the impostor doesn't fight - instead running away. Spidey follows him into an abandoned warehouse. His Spider Sense goes of and he dodges a few gas blasts, but soon the warehouse is filled with gas and he goes unconscious. When he gets up, he cannot place his location. He walks around a little, and realizes he has shrunk! (straight from Amazing Spider-Man vol. 1 067) After a panicked sequence featuring him trying to figure out what has happened and what to do and escaping from hallucinogen induced hazards and monsters, Spidey finally loses his witty facade and breaks down pleading fro help. He just hears an eerie laugh in the background. As "death" nears him, Spidey hears a ghostly voice saying "With great power comes great responsibility". He gets up and fights. Soon, his amazing strength starts ruining the entire set. As the set breaks down, so does the illusion, until Spidey sees Mysterio right in front of him. He punches Mysterio once, but Mysterio teleports away. We get a glimpse of Mysterio's life and learn a little about him. As the scene ends, we see a small spider device stuck on Mysterio's helmet. In his bedroom, we see Peter working on some science stuff while Aunt May tries to get him to stop studying and do something else. We see the beginnings of a lightweight and compact gas mask and new lenses for the costume. Peter's experiments cause a little damage, etc. In between all this (as Peter lies in wait, we see more of his school life). One night, Spidey's spider tracker causes a ping on his smartphone. He quickly changes the frequency to that of his Spider Sense and slips into his new, upgraded costume to get there. He ambushes Mysterio, but Mysterio teleports them both into his base before Peter can react. He tries to gas Peter again, but the new mask protects him. But Mysterio had a backup plan. He starts assaulting him with attacks, both illusionary and real. However, Spidey's special new lenses can view light, infrared and ultraviolet at the same time, so he sees through the illusions and is beating Mysterio with ease until the lenses crack. Then, Mysterio makes his biggest illusion yet - a team of Avengers who all set upon Spidey. They have a huge fight until Spidey beats them all and webs Mysterio to the ground - with a note, of course - and calls the police. He gets home tired and bruised - then realizes the science expo is the next day. he has no ideas at all, but as he is about to give up, he realizes that his Spidey tech could be useful in other situations. He slightly reworks the new lenses into sunglasses that can view UV rays, IR rays and light rays, then calls it a night. He wins the science contest and is picked to be a intern at Horizon Labs. The ending of the movie could be Aunt May asking if Peter had got the eggs yet. Peter says they're in the fridge (inside joke to TASM movie franchise). The post-credits scene is of Peter preparing to ask Gwen out on a date when he hears the doorbell ringing. He opens the door, and there stands Mary Jane Watson, new to the neighborhood! Of course, there should be several guest appearances from JJJ as Peter sells photos throughout the movie.
AVENGERS INFINITY WAR (PARTS 1 AND 2):
After hearing about the scope of the threat, Spidey and Stark work together to upgrade their tech and also sit with the other Avengers to discuss strategies. Spidey builds his Ends of the Earth suit (it shouldn't be referred as that in the movie though) so he can breathe in space. It also has some extra benefits of enhanced strength and durability, cyro-pellets, magnetic webbing (since normal webbing doesn't work well without gravity), complete invisibility and undetectability, immunity to sonic attacks, some other web types, flight, repulsors and enhanced lenses and heartbeat detectors.
It works well, but in Infinity War Part 2, it should be destroyed and Spidey should find the symbiote, which enhances all his physical attributes to greater degrees, but without the extra tech features. Overall, Spidey's role in the movie shouldn't be TOO large - I think it should be a lot of homage to the original movie Avengers before the new Avengers start to take over in sequels to this.
Peter's personal life is going pretty well, as the bullies have cut down on their bullying, Peter no longer has to work as hard for money, and he is dating Mary Jane. He is gelling with the scientists at Horizon as well as improving his photography skills for the Daily Bugle as a part-time job. Most of the world is now siding with Spidey due to his role in Infinity War. However, the symbiote is affecting his attitude towards crime, as he is becoming a more aggressive hero. Many criminals are being badly beaten. JJJ's distrust is growing to the level that he will do anything to stop Spider-Man. Meanwhile, journalist Eddie Brock is gathering dirt on Spidey's activities to portray him in a bad light to the Bugle. Eddie's greed is leading him to use false evidence to ruin the wall crawler's reputation. Jonah finds a sympathetic figure in Norman Osborn, father of Spidey's classmate Harry. They discuss a plan to genetically engineer Spidey's replacement - a "scorpion". However, Scorpion goes rogue as he has second thoughts and wishes he hadn't been turned into a genetically modified creature. The movie could then show Peter saving JJJ multiple times due to Scorpion attacking him, which also develops Scorpions grudge against Spidey, as well as showing the extent of Spidey's compassion). Meanwhile, Norman starts getting intrigued about Spider-Man. He begins to use his resources in an attempt to find his secret identity. When Scorpion begins to rampage across the city, Spidey confronts him. Despite the upgrades the symbiote gives him, Scorpion's strength proves to be stronger, and his mechanical tail is a huge advantage. After being badly beaten, Spidey notices Eddie falsifying evidence against Spidey to use in his next article.
He is already angry, and he calls Eddie out on it in public. This causes Eddie to be fired and lose his credibility. Peter decides to ignore his friends and family and works on upgrading his web fluid on Horizon Labs. After sneaking back home, he notices that Aunt May is crying. He quickly true to comfort her and we find out that she is gelling neglected and feeling like she is inadequate for Peter due to the lack of time Peter spends with her. This is when Peter realizes the symbiote has been influencing him and casts it off. It goes onto Eddie. The next day, Spidey gets a ping from his spider tracer and follows it to Oscorp. Scorpion has kidnapped JJJ and Osborn and is ready to kill them. Spidey saves JJJ immediately and engages in a furious fight with Scorpion, eventually webbing him up. During the fight, Osborn is knocked into some chemicals and turns unconscious. Of course, JJJ blames Spidey. At home, Peter has to pay also. Mary Jane breaks up with him to go out with Harry. He is very behind on his school work. Harry now hates Spidey for failing to save his father. However, Gwen address to go out with Peter. The movie ends with Peter getting ready to sleep as we see a strange black silhouette on his ceiling. The post credits scene is of Osborn in the hospital. He wakes up and his eyes are pure green/yellow. He blinks, and they are back to normal.
Open with a small time crook being stopped in the middle of a crime and being webbed up. Cut to Peter sleeping at his home. A clue that Peter was not responsible for catching the thief. The next day, he meets up with Gwen to go on a double date with Harry and Mary Jane. However, he ditches the date when he sees reports of a new superhuman menace on Manhattan. Harry is beginning to feel quite angry with Pete's constant disappearing acts. When Spidey gets there, he sees Time Square in darkness, with one glowing figure levitating. 'Hello Spider-Man, I am ELECTRO!' He says. Spidey quips back and webs him in the face. The battle starts but it goes badly for Spidey. He eventually gets electrocuted and falls unconscious.
He wakes up in a secret underwater base. 'Hello, Spider-Man. I am Doctor Octopus,the leader of this motley crew.' Spidey quips back, but he gets hit with a mouthful of sand. He sees that Electro and a guy made of sand are both standing near Ock. They are his creations. He tries to break free, but the shackles are vibranium. Ock mentions his plan is to take blood from Spider-Man in order to engineer an army of superhumans who follow his will. He will use them to conquer the world! He takes the sample, analyzes it on his computer and sends it to enter location. He then leaves Spidey alone in the base and let's the water begin to leak in. As Spidey is struggling, we see a quick black silhouette open the shackles. Spidey is free, but he doesn't know what just happened. He decides he has to track down Ock and stop his plan. He goes to Horizon and begins upgrading his suit with electroproof material, and he makes more cryo pellets. Also, he modifies the cryo pellets into a cryo cube that can be used to carry organs. This earns him a job offer at Horizon from Max Modell. He accepts as a part timer until he graduates. Finally, he creates an algorithm on his smartphone to notify him of any superhuman trouble. As he sleeps, the camera closes into a black silhouette on the ceiling - we see it has a white spider symbol. His spider trackers find suspicious signs the next morning. Since it is a weekend, he doesn't have to worry about school, and notifies Aunt May before leaving. He sneaks into an abandoned factory warehouse and he sees that Ock has kidnapped many people! He abandons the stealthy approach and attacks Ock with anger. However, Ock's cronies take the bow for him, then attack back. Electro is quickly dispatched as his attacks have no affect and he can no longer hurt Spidey due to his upgraded costume. Sandman proves to be a larger challenge. The cryo pellets don't affect him as Spidey had earlier thought and he overwhelms Spidey with his powers. Spidey is drowning under the sand when he makes a last ditch effort by switching in his special corrosive webbing cartridges. It works. The individual sand particles start dissolving as Sandman screams. Spidey leaves him incapacitated as he moves on to Doc Ock. He dodges a few tentacles and one-shots him. Insert funny quip. But Ock remotely triggers the spider serum injections. Thankfully, Spidey's spider speed enables him to destroy all of the syringes in a fraction of a second, saving the hostages. But then he is attacked by a young boy of around 13 years of age. The boy starts beating on Spidey and Spidey realizes that he has powers - very similar to his. Doc gloats on how he had a hidden test subject just in case. The boy pleads with Spidey to stop the mind control before it is too late. Spidey dodges the attacks and for back to Ock. He demands to know the location of the mind control device. When he funds it hidden deeper in the lair, he is forced to hack into it and disable it from the inside. Ock is shell shocked. He says, "Impossible! No one can hack my codes! Who are you?" Spidey disables it and deletes all the data. "I am... The Amazing Spider-Man!" Now that the young boy is no longer under mind control, Spidey talks to him before calling the police to clean up. He says his name is Miles... Miles Morales.
Spidey asks him whether he wants to come to his lab and let Spidey try to cure him, but Morales declines. He says that Spidey is his hero and now he has the chance to emulate him. Spidey says okay (paving the way for a Miles Netflix series) but takes a vial of his blood (on case he ever needs to stop him). He swings home, battered and bruised. The post credits scene could be a teaser for a Netflix show on Miles.
This film is all about Spidey vs Venom, with a few distractions for Spidey's school life, some time to plan at Horizon, and some time to make sure everyone he loves is okay. It starts off with Peter walking to class. Suddenly, he is pushed in front of a speeding car! He told to the side before being run over, but pedestrians for to his aid and Aunt May comes to take him home. He is worried about how his Spider Sense could have failed. When he gets home, he sees a notification on his phone. He plays back a creepy voice message telling Spidey to come to a warehouse alone. Spidey goes to the warehouse at night, all his senses on high alert. However, he gets captured and knocked unconscious. He wakes up bound in a giant web, with a monster leering at him. "We are VENOM!" Venom explains his motivations and how he knows Spidey's secret identity. He says that he wants to play a game with Spidey - one with only one ending: Spidey's death. If Spidey goes to the Avengers, Venom will regretfully kill Aunt May (Venom's personality as a protector of innocence should also be portrayed). He let's Spidey go and theirs him out of the window. The rest of the movie should be suspenseful and slightly scary. Spidey would be trying to find out more about Venom and Eddie, all while trying to keep away from Begin and not let him know what he's doing. It should be similar to the 'Venom Saga' in the 90s Spidey show, as Venom randomly pops up to humiliate Spidey while Spidey goes about his business - his games getting more and more dangerous and lethal. However, Venom should never hurt any innocent people, as he should say that he is a defender of the innocent and Spidey is the bad guy. In one of their fights, Spidey should be able to take a sample of the symbiote. He goes to Horizon and analyzes it, finding out its weakness to sonic and fire. As such, he creates a few cartridges of unstable fire webbing and he creates a sonic weapon. Now, he just continues with his crimefighting, waiting for Venom to ambush. When Venom ambushes Spidey, Spidey hurts him badly with the fire webs.
This enrages Eddie and he uses the symbiote to destroy Spidey's web shooters. Spidey still had the sonic device but he is not given a chance to use it as Venom goes on a rampage against him. He is busy trying to dodge when Venom hits a water tower off a building. Spidey can't stop it as his web shooters are broken, but he so tries. However, Eddie momentarily calls and whispers, "Ann?" Eddie jumps to the rescue and hoists the water tower back up. Spidey remembers that Ann Weying was Eddie's ex-wife. Eddie realizes that he was the one endangering others while Spidey tried to save them and forgives Spidey. He says that he will move away for a while to become a hero. As Spidey leaves, he is secretly sprayed by a gas. Spidey changes into civilian clothes outside his school, unaware that he is being watched. The shot zooms out as we see a man dressed in green and purple say, "Spider-Man is... Peter Parker?" The post credits scene could be set up for a Venom movie and it could show Venom trying to be a hero in San Francisco.
This is all out war for Spidey. Norman Osborn buys out the prison in which the metahumans Spidey has fought are kept. He secretly visits then and organizes then into a group united by one thing - their hated of Spider-Man. One night, he helps them get free. Mysterio, Doc Ock, Electro, Sandman and Scorpion are free once more! Meanwhile, Peter had no clue of these sinister ongoing, instead preparing for prom with Gwen and then his graduation! However, Spidey has to make an assistance when he sees Doc Ock in the middle of Manhattan threatening civilians. He immediately apologizes to Gwen and swings away. When he gets to Ock, he is outmatched. Electro gets him by surprise, then Ock hits him with a tentacle, Sandman smacks him with a blast of sand, Scorpion snags him with his task and Mysterio traps him. Spidey asks then why they are working together. Doc Ock answers, "We have joined together for the common cause of defeating you. We are..." "THE SINISTER SIX!" finishes a fast moving gray mass who rams into Spidey. "Like my newest creation? I call him... The Rhino!" This should the most brutal battle of the series. Meanwhile, Gwen is alone in her house. Suddenly, a mashed figure swoops in. He takes Gwen and knocks her unconscious as she tried to scream. Spidey is struggling to think of a way out of his predicament. Six of his toughest enemies, all allied together? Just as Ock is about to deliver the final blow, Spidey goes with an old trick - web in the eyes. He is able to distract the villains long enough to escape down the sewers and make his way into Horizon Labs. He gets to work covering each one of the Six's abilities, as well as upgrading his tech. Meanwhile, we get a glimpse into Osborn's tortured psyche as he interacts with his 'disappointment' of a son, Harry and as he interrogates Gwen about Peter. Finally, Spidey is done with his work. He dons a majestic new suit (created for the movie) that is perfectly suited to taking the Six down.
When he emerges, the Stuff are terrorizing Manhattan looking for him. "You want me? You got me!" Spidey tanks lightning from Electro and then shirt circuits him. He blowtorches Sandman into glass. He punches Rhino out using his upgraded strength and durability. He rips off Scorpion's tail. He is immune to Mysterio's illusions, so he just one-shots him. He prepares to do the same to Ock, but is blocked. "Impressive display, but did you really think you could take me out that way again? You see, I have upgraded my tentacles to vibranium and I have genetically engineered myself to have superhuman attributes equal to yours." Now a tough battle begins, with Ock slowly destroying Spidey's new suit. By the time Spidey wins, the suit is pretty much destroyed. Spidey is ready for a nap when he heard cackling from above - it's a new villain who is holding Gwen hostage!
Spidey chases him to the bridge. They fight and Spidey gets the Goblin (I think he should just be called the Goblin rather than Green Goblin in the movies) to drop Gwen. As he had the upper hand, he unmasks the Goblin. He is shocked to see Norman Osborn, his best friends father. "Hello Peter" Peter asks him why, why Norman is trying to attack and kill Peter. Norman snaps and says, "Because I am the Spider's archenemy for now and ever!" He then throws Gwen of the bridge, leading to Gwen's death. This causes Spidey to get extremely angry and throw Osborn into a nearby warehouse where the fight continues, Osborn is losing and is getting pound to a pulp as Peter loses control. Finally, Peter s short with Osborn on the brink of death. He gets to deliver the final blow, but doesn't, remembering the lines, "With Great Power Comes Great Responsibility" Suddenly, Osborn laughs and nicks him and disappears in a puff of smoke. Peter goes home where Aunt May, Harry and MJ fail to cheer him up. After Harry and May leave him to himself, MJ is the only one who stays. Peter and her bond together over their love for Gwen as the movie ends. The post credits scene shows Peter and his friends graduating from high school in a glum and depressed atmosphere.
BONUS ONE-SHOT THAT TAKES PLACE AFTER SPIDER-MAN 2: THE BURGLAR
Spidey finally tracks down and confronts the burglar who killed Uncle Ben. Lots of reflection on Ben's death and a lot of thought about morality as Peter wrestles with his feelings and tries to decide whether or not to kill the burglar who killed Uncle Ben.
So I think this would be a great arc for Peter over the films as he matures from a immature whiz-kid teen superhero into a hero who has done it all and is worthy to lead the Avengers. What do you think?