Probably way off what will happen but based on how they have handled the MCU Peter and what was set up in 2 this is what I would go with. Have the movie be called Spider-Man: No way home.
Jameson's confession is being taken at face value by most people and peter is declared a public enemy, pete is kicked out of school, his home is attacked and May is forced to move to a secure location w/ the help of Happy.Ned and his friends are all unable to talk with him because they are in danger and moved away to protective custody. MJ really wants to help Peter, but he pulls one of his classic moves from the comics and pushes her away to "protect" her. Early scene in the film could be Peter still trying to serve as a hero despite his fugitive status and attempting to stop a gang war (maybe feature a character like hammerhead or tombstone) but while trying to stop it Peter is confronted by the police who attack him instead of the criminals and they escape.
The Avengers are unable to step in to help Peter because they essentially don't exist anymore ( based on the movies that would come out before Spidey 3 would there aren't many ways for the avengers to be reestablished). The incident with the gang war is used against Peter and the media twists it that he got in the way of the Police stopping the violence. After that incident and the building pressure against Spidey, the new owner of the old avengers tower is revealed to be Norman Osborn and he comes out and states he feels a responsibility to step up in the absence of the avengers so he creates a new team of "heroes" and their top priority will be to take down Spider-man.
Team could basically be the sinister 6 though they aren't called that in the movie and include Vulture (who receives a pardon because the media is now twisting it as Peter was the villain in the first film and vulture is painted as a hero who tried to stop him, Scorpion (who could receive a pardon or something like that which makes him free). Have Rhino, Shocker, Kraven and Hobgoblin ( who would be seen as the leader of the team) round out the team. ( I would use a goblin in the movie but not osborne, I would leave him as the physical threat to Spidey for another film). Norman just plays a sort of corrupt tony stark background role in this movie. In addition to hunting Peter the sinister 6 are actually fighting crime at the direction of Osborne but are mainly focusing on taking out cells of supposed terrorists that have suddenly shown up and are alleged to be led by alaistair smythe.
Bulk of the movie is basically Peter being pushed to his limit and being all alone for the majority of the film. He is pushing away everyone in an effort to protect them. He could have a few battles with members of the sinister 6 individually and always ends up being challenged but ultimately escaping. Maybe have a scene where he goes to visit uncle ben's grave and talks to him saying that he is sorry and feels like he has failed uncle ben all over again and feels the only way he can honor uncle ben's memory is by taking this all on himself and not putting his family in danger.
Soon after that Peter gets confronted by all 6 of the villains and is almost killed but is saved at the last second by Rhodey( which keeps the iron man connection and makes sense to me, because MCU likes to include one other character in the spidey films and it makes no sense that Rhodey would not help his best friends protege) Rhodey takes Peter to the safe house where May and Happy are and they have an emotional conversation about how Peter needs help, Peter lashes out saying he has to be on his own to protect them because anyone he values is in danger or dies because of him. We finally get mention of uncle ben's death and he confesses to May what happened and that Ben Died because of him. Peter appears to be going off on his own again, when MJ and Ned show up and talk to him as well. Ned and MJ reveal that while they have been away from Peter they have been teaming up doing some research into Osborne, using Ned's hacking skills and MJ actually doing some investigating (kinda like in the PS4 game). MJ reveals that the"terrorists" that the sinister 6 have been fighting are actually old rivals of osborne and that he is planning on running for mayor but wants to make sure that smythe is out of the way before that happens. Using that info and her connection to Peter MJ is able to convince Peter that he needs to be with them and not push them away, that they give him strength and are not a weakness.
Peter is inspired by their faith in him and using their input along with his own observations from previous fights he creates a new suit that tackles the physical strengths of the sinister 6 (probably something that looks like the ends of the earth armor). Peter and Rhodey team up together to fight the sinister 6 and we get an epic battle, during the battle the sinister 6 get the upperhand but right when one of the members goes in for a kill shot on Peter, the Vulture has a change of heart and helps Peter and Rhodey and they are able to defeat the sinister 6. Vulture gets mortally wounded but is able to record a message that gets released and essentially exonerates Peter, a confession or something like that which reveals that he really was a villain and that the sinister 6 were never actually heroes and that Peter was the only way they were stopped. This kinda twists the media narrative a bit and Spider-man is seen more as a hero but still has Jameson leading the charge against him and Osborne is able to disassociate himself with the sinister 6 by claiming that the hobgoblin corrupted the team from it's original intent. Peter is reunited with his friends and family. He gets engaged to MJ and they agree to live together. End of the film is Peter meeting with Rhodey, FalCap, Black Panther, Wasp and Banner and he convinces them to restart the avengers. Peter, Mj and May are living at avengers tower at the end of the movie.
End credits scene is Osborn collecting a blood sample of Peter's that was left behind at a battle, hinting that he might create a clone, we also get a peak at the green goblin armor. Second could be the vulture gear being handed over by Osborne to Blackie drago who becomes the new vulture with hints that Osborne still has plans for a future version of the sinister 6.
(Sorry for the book - have way too much time on my hands due to a broken leg that is forcing me to be on bed rest for a few days)