Okay, so I decided to go ahead and take a stab at a detailed plot for SM3 based on many of the things we have speculated on. I'm going to base this plot outline on a few elements: the things that have been confirmed, a bit of the Q&A, and a few "personal fantasy" elements. Again, I do not think this is "OMG! Brilliant". I am simply putting together my own plot out of the scattered bits of rumors and confirmations we have.
Here it goes:
-The film opens with Peter buying MJ's engagement ring; he has decided to propose to her tonight and will do so at dinner after MJ's big broadway debut.
-As Peter is on his way back to the apartment where he and MJ live together, he encounters someone trying to rob an armored truck. In his Spidey gear, he swings down to stop them only to discover the incredible power this mystery man possesses. After some mayhem and chaos, the powerful robber gets the best of Spidey and our webslinger's mask is ripped off. Spidey escapes, fearing his identity will be revealed on the streets.
-Peter, exhausted and strained after that battle, returns to the apartment where Harry is talking with MJ, seemingly waiting for Peter. Some mind game action here...
-Peter attends MJ's play, but Harry is also in the audience...
-Outside of the theatre, Peter is on his way to the restaurant when someone cries out for help in a dark alley (remember the burning building scene from SM1). Peter enters the alley, and suddenly the figure punches him sending him back. The figure is none other than a darkly clad Harry (in a non-Goblin-esque getup). Harry hops on a glider and grabs Peter as they fly into the air. Harry says he wants to kill Peter right in front of MJ at the restaurant. Peter fights back and eventually they tumble down into an alley and Harry is injured badly.
-Peter takes Harry (out of the costume) to a hospital.
-We see Peter back at the apartment. MJ confronts him about where he was, but Peter of course can't tell her the truth about Harry, and MJ is upset (for various reasons blah blah)
-The next day at the Bugle, JJ is working on the top story, "The Sandman Defeats Spider-Man", when Peter shows up picture-less. (Here we'll learn a bit of the "origin" behind this guy, Flint Marko). Eddie Brock enters and we get a glimpse of the relationship between Eddie and Peter (rivalry). Eddie has a picture from the fight: a blurry picture of Spidey without his mask. Some JJ/Peter/Betty/Robbie/Hoffman/Eddie banter, and Peter leaves. JJ orders Brock to investigate Peter, blah blah (you know what the deal is here).
-At the lab where Peter works for Dr. Connors, the good doctor introduces Peter to Peter's new partner, Gwen Stacy. Connors introduces his two pupils to his program's greatest experiment, a possible cure for cancer (WINK, WINK).
-Later, Gwen and Peter are working on some science shiznit and the two are hitting it off well. Peter walks her home, and she introduces him to her father, the police captain. The Captain invites Peter to stay for dinner, and Peter stays (cue dinner talk scene where we establish the fact that the captain is a nice, good guy). As Peter is leaving the house, we see Eddie pull up. Eddie and Gwen use to date. Peter is leaving the house. Eddie was hired to investigate Peter (you see where I'm going with this??)
-We enter the Marko home and find Flint in a dingy home with his wife. We learn about Flint's daughter's illness; she is dying. (Cue dramatic piano music). We also learn that word of Connors' and his staff's project has been leaked in the news...
-MJ (hearing that Harry is in the hospital) goes to visit him. Aunt May is there as well. The two have a brief talk about MJ/Peter's relationship (Aunt May taking on a motherly role for MJ giving her advice; we also see a hint that May knows that Peter is Spidey).
-At the lab, Peter, Gwen, Connors, and the staff are working and observing the symbiote, when Peter's spidey sense goes off and in comes the Sandman. Peter changes to Spidey, there is a quick battle, and eventually Spidey gets the symbiote on him. Flint escapes.
- At night, MJ and Peter are in bed together (don't get any ideas). Peter is having some nightmares, imagining a black ooze devouring his friends and family (there is some ominous shiznit with Uncle Ben, yatta yatta). Peter wakes up, and decides to go out and swing to get his mind off the visions. He swings towards a building and sits next to a gargoyle. It begins raining, and suddenly he looks down at himself, and his suit is all black and he can't get this dark substance off...
-Flint's daughter dies. Flint is shattered by this, and decides to destroy everything that reminds him of the happiness she once brought him...
-The next day...Coney Island! Peter is trying to bring a little joy back into his relationship with MJ, and he has the ring in his pocket. We also notice that Eddie Brock is taking pictures of Peter at the park. There is a big event here at Coney Island, and Captain Stacy is there with Gwen. Gwen eventually comes over to Peter, and we get an awkward moment between Peter/Gwen/MJ. Eventually Sandman shows up, and Peter leaves MJ to do his Spidey thing. As he opens up his shirt, he is reminded of this new black suit. He doesn't seem to think anything major of it, and he changes. Flint is about to attack a roller coaster when the new black suit Spidey attempts to stop him (a good action packed sequence ensues). Captain Stacy goes to save a little boy from falling metal. Spidey goes to web the metal before it lands, but his webs don't respond accurately. Captain Stacy gets the boy out of the way, but is crushed in the process. Gwen finds her dead father, and is devastated. Eddie Brock tries to get some pictures of the event, but in the course of the fight, his camera is destroyed when Spidey sweeps in to stop an object from falling. Eddie is a bit pissed (WINK, WINK). Flint sees the destruction he has done, and escapes. Gwen is left kneeling by the body of her father...
-At the Bugle, the big story is "Black Spider-Man Kills Police Captain". Peter enters, and JJ is again pestering him about pictures. Peter gets pissed and quits the Bugle.
As Peter is leaving, Eddie (ticked off) confronts Peter about the situation at Gwen's house and what he was doing with her at Coney Island, and Peter pushes Eddie away warning him to leave him alone. (Another sign of the growing darkness in Peter).
-At the apartment, MJ comes home from another performance of her play (which Peter didn't attend). Peter is at the apartment trying to figure out if his powers are going beserk again (like in SM2). MJ wants to know where he was, and Peter snaps at her. She questions whether or not they were truly made for each other, and Peter simply can't take it anymore and just leaves.
-A car jacker steals a woman's car, and Spider-Man (in the black suit) swoops in to stop him. Spidey jumps onto the car and rips the top off of it. The car jacker is swerving on and off the road destroying newsstands and nearly running people over. Spidey grabs the car jacker out of the car and begins pummeling him, but suddenly stops when he realizes what he is doing. He looks at his hands and realizes something is not right with him. He swings away.
-Gwen Stacy is on the news calling for the arrest of Spider-Man. The city is now growing against the webslinger.
-Harry, at the hospital, begins to hear the voice of his father, again...
-Flint is at his home where his wife is preparing to leave him for good, unable to take the fact that her husband has turned into a monster driven by the pain of their daughter's death. She warns him to stop what he is doing before it's too late, and he warns her not to leave him. She refuses to stay with him and tries to walk out, but before she can, Flint (in anger and unable to control his powers) fills the entire home with sand, suffocating her inside. Flint is horrified by what he has done, and seeks to end what he has become.
-Connors is working in his lab, when Spidey in the black suit arrives. Peter peels the mask off his face and Connors is shocked. Peter demands answers and Connors tries to figure out how to get the suit off. Connors has no solution. Suddenly, Flint enters demanding a cure, and Peter (without his mask) lunges after him. The two are duking it out, but we notice that Peter is somehow stronger than we've ever seen him before. Then, as Sandman makes a move to strike Peter, a tendril flies out from the suit and stabs Flint. Suddenly, Flint begins to crumble to pieces, and his sand body disperses through the cracks in the floor. Flint "dies" a man misguided by what he thinks is the right thing to do with his power.
-Peter goes to Aunt May's only to find that Eddie is there talking with her. Peter is infuriated.
-Eddie is at the Bugle at night working on a story, when Spidey shows up and threatens him to stay out of Peter Parker's life. Then Spidey destroys Eddie's computer and disappears. Eddie is completely shocked, and now has an ultimate hatred and suspicion of Spidey.
-Mary Jane is visiting Harry who is still in the hospital, but is doing much better. MJ tells him that she and Peter are not working out, and Harry offers her his love. MJ denies him (in a nice way of sorts), and leaves telling him that she appreciates him as a friend. Harry is beginning to come back to his full senses. He begins to hear the voice of his father again. We get a great scene here with the Goblin/Norman spirit talking to him. Harry then sees the report on his hospital TV about Gwen wanting Spider-Man turned in. He escapes the hospital.
-Harry is in the "Lair/Lab" following his father's words in his head, and is injecting himself with multiple doses of the serum. He grabs his father's original Goblin mask and suit...
-Gwen is at her home, and hears a noise on her balcony. She goes out to see what it is, but finds nothing. She walks back into the house and finds Harry in the Goblin suit (no mask) standing there. Frightened, she falls to the floor and crawls back. Harry asks her if she wants to meet the man who killed her father...
-Peter has a heart to heart with Aunt May who gives him a compelling speech about power and how no matter how much you have, some things you can't control...
-MJ is packing her things in the apartment when she hears a knock on the door. It is Eddie Brock demanding that MJ tell him what Peter's "secret" is. Suddenly, a blast rips half of the apartment off and Harry in the Goblin suit (no mask) snatches up MJ and drops a note on the floor. Brock looks at it, and suddenly Peter arrives and is stunned by the sight. He looks at the note which reads, "The church...bring the costume" (The costume is referring to the Spidey suit in general and NOT the black suit which Harry knows nothing about at this point).
-At the church, Peter arrives in the black suit, where he finds MJ and Gwen tied to the bell tower high above the ground. Suddenly, Harry appears on the glider with the Goblin mask in hand. Eddie sneaks inside the building (apparently having followed Peter somehow) and hides underneath the bell tower. Harry reminds Peter that this is the church Norman's funeral was held in. Harry puts the Goblin mask on and flies after Spidey, and the two duke it out in a massive aerial duel over and around the church. Eddie Brock gets to the top of the belltower and gets to the girls. He releases Gwen, and tries to leave with Gwen while MJ remains tied up. Suddenly, a bomb from the fight goes off nearby Eddie and sends him plummeting to the ground, while Gwen is left hanging on the side of the tower, hanging on for dear life. Eddie lays on the ground dying.
Peter and Harry drop into the dark church and battle hand to hand. Although Harry is stronger than his father's version of the Goblin, Peter gets the upper hand with the symbiote and sends Harry flying into a wall and rocks collapse on him. Harry rises from the rocks, and lunges at Spidey and begins beating Spidey down, until suddenly he clutches for his chest and begins to cringe in pain. Harry collapses to his knees. He is dying from the overdose of the formula. Harry whispers to Peter, "The tower..." and starts to fade.
Peter arrives at the top of the belltower and helps Gwen up, when suddenly his Spider Sense goes off and a concussion bomb which had been planted nearby explodes, damaging the tower and causing the massive bell to ring. Suddenly, the symbiote begins to peel off Peter and falls down to Eddie smothering him in the black ooze. Peter now remains with remnants of his red/blue suit clinging to his body. MJ's rope snaps and she begins falling to the ground. Peter shoots a web to her feet to grab her, and she stops falling. He sets her down, then goes down to make sure she's okay. But...she's dead. Her neck had snapped...
Peter is devastated beyond belief. His best friend and the woman he loves are gone...
-In the aftermath of the battle, the police search around the damage. They stop at the bell tower and find a puddle of blood under the tower, but no body....
-Peter attends the funerals of both Mary Jane and Harry, accompanied by Aunt May .
-At May's home, Peter is visited by Gwen. They hug, both carrying so much pain and tragedy. Peter realizes that she is someone he can possibly confide in...
THE END.
