At the abandoned warehouse by the pier, the villains were working on the machine.
Mary Jane: Hey! Hey! I'm talking to you! You got what you needed for your little science project, now let me go.
Mojo Jojo: What? And let you bring the police?
Doc Ock: He's right. Not that anybody could stop us now that Spider-Man's dead.
Mary Jane: He's not dead. I don't believe you.
Doc Ock: Believe it.
They got the machine up and running, unaware that the heroes were close behind. They snuck quietly to Mary Jane.
Spider-Man: (quietly) Surprise. As soon as you get free...
Doc Ock's robot tentacle hits the pipe and the gang dodged out of the way.
Doc Ock: I should have known Osborn wouldn't have the spine or the guts to finish you and your friends!
Blossom: Shut it down, Ock.
Leni: You'll hurt a lot of people this time.
Doc Ock: Well, that's a risk we're willing to take.
Spider-Man: Well, we're not.
They tried to get to the machine, but the villain flung them out. Luckily for them, they got back in and began their fight with the villains. The Ninja Turtles and Sonic circled around Eggman's mech.
Sonic: Keep going!
Dr. Eggman: Move all you want. We're still going to stomp you into blue and green jelly.
The Girls were busy battling Mojo in his robot.
Blossom: Power Yo Attack!
The yoyo hit the monkey, but he kept up. Bubbles then fired bubbles.
Bubbles: Sticky Bubbles!
She shot sticky bubbles at the robot, but it got off.
Buttercup: I'll show you!
She swung her hammer at the robot, but it didn't make a dent.
Buttercup: What happened?!
Mojo Jojo: We thought you'd try to do this stunt again, due to my Robo Jojo being destroyed by that train, Eggman built me this new nearly indestructible Robo Jojo to shrug off your foolish attacks. I called it the ROBO JOJO 2.0!
Powerpuff Girls Z: Oh, dear….
Meanwhile, as the battle raged on, the Louds were sneaking their way to the machine.
Lincoln: Almost there, girls. As soon as we get to it, we're gonna shut it down once and for all.
Luan: The good thing is that Otto, Mojo, and Eggman are too busy to deal with us.
Lori: That's great. (sees something scary) But who's dealing with him?
Stripe: Lincoln… BAM!
He fires rounds from his pistol at the gang. They avoided it, but were inches away from the machine. Soon, the machine starts to make the little sun grow and sucks up some parts of the warehouse. It was starting to suck up everything, with Mary Jane about to be sucked in.
Spider-Man: Hang on, Mary Jane!
He punched Ock in the face and soon he saved Mary Jane from her death.
Spider-Man: Run! (Gets hit by a pole from Doc Ock)
Doc Ock grabbed the hero by the foot.
Doc Ock: Let's see you scurry out of this.
As Ock was about to stab Spider-Man with his robotic tentacles, Spider-Man grabs the cable line and Doc Ock got shocked by stabbing it causing the robot tentacle remote control to malfunction.
Remote control computer: Danger. Danger. Malfunctioning. Self-destruct activated.
Dr. Eggman: Self destruct? (The remote exploded) Uh oh.
After Spider-Man pulls the cables out, the sun was still growing.
Spider-Man: Now what?
Back with Lincoln and his sisters, they were still hiding as Stripe was firing rounds at them.
Lola: How are we gonna stop him now?
Lincoln: I don't know. Usually it's sunlight or electricity. What's there to… (sees some electrical cables and gets a lightbulb idea) Gizmo, can you do it again?
The cute mogwai nodded, for Lincoln had a plan. He ran out of his hiding spot.
Stripe: Gizmo! Bam! Gizmo caca!
Gizmo ran for the electric cables.
Gizmo: Bright light! Bright light!
The gremlin was about to fire when the mogwai managed to get to the cables. He pulled them off and the unplugged cables landed in the water. This caused the water to be filled with electricity, electrocuting the nasty gremlin. Parts of his skin melted off more and more until Stripe became nothing more than green goop.
Luna: Wow, you did it, little guy.
Lincoln: Good job, Gizmo. (pets Gizmo on the head)
Lisa: Now to take care of business. (Sees the green goop gets sucked into the sun; scared) Starting with that.
Meanwhile, outside of the warehouse, some of New York was about to be sucked into the sun. Doc Ock wakes up with his tentacles short circuiting. Spider-Man and Lisa approached the man.
Lisa: Dr. Octavius, we have to shut it down.
Spider-Man: Please tell us how.
Doc Ock: Why should I help you?
Spider-Man: Because… (takes off his mask) It will destroy everything if we don't stop it.
Doc Ock: Peter Parker? "Brilliant but lazy."
Lisa: Look at what the machine is doing. We must destroy it.
Doc Ock: I can't destroy it. I won't. (grabs the two with his tentacles)
Peter: You once spoke to me about intelligence. That it was a gift to be used for the good of mankind.
Doc Ock: A privilege.
Lisa: Those things are turning you into something you're not. Don't listen to them.
Doc Ock: It was my dream.
Peter: Sometimes, to do what's right, we have to be steady… ...and give up the thing we want the most. Even our dreams.
Doc Ock: You're right. (to his robot tentacles) They're right.
His robotic tentacles were about to convince him otherwise, but he won't stand for it.
Doc Ock: Listen. Listen to me now. Listen to me now.
He got them to simmer them.
Lisa: Now, tell us how to stop it.
Doc Ock: It can't be stopped. It's self-sustaining now.
Peter: Think!
Doc Ock: Unless.. The river. Drown it.
Peter was about to do it, but Doc Ock stopped him.
Doc Ock: I'll do it.
He approached the machine with readiness and caution. Peter looked back and saw Mary Jane. But then, some support beams were about to fall on her.
Peter: Noooooooooo!!!!!
He came to her rescue, stopping the beams from falling onto her.
Peter: Hi.
Mary Jane: Hi.
Peter: This is really heavy.
Doc Ock got under the machine and pulled at the support beams.
Peter: M.J. In case we die...
Mary Jane: You do love me.
Peter: I do.
Mary Jane: Even though you said you didn't.
The former villain pulled the machine down.
Doc Ock: I will not die a monster.
With all his strength, he pulled it down into the river, along with him and the entire warehouse. He was once human, then became a villain, and now, he redeemed himself by sacrificing both his work and himself. With the others, they were all safe. Lincoln cradled the mourning Lisa, for Otto made things right for both her and the world.
Mary Jane: I think I always knew… ...all this time… ...who you really were.
Peter: Then you know why we can't be together. Spider-Man will always have enemies. I can't let you take that risk. I will… ...always be Spider-Man. You and I can never be.
When the police cars arrive, he dropped off Mary Jane and left, along with his friends. John Jameson arrived.
John Jameson: Mary Jane!
They hug, now that Mary Jane knows why Peter can't be with her. He was Spider-Man, and he doesn't want her to be the target of his enemies. Peter and his friends quickly leave the scene. Back in Harry's mansion, he couldn't believe that Peter was the Spider-Man that killed his father. Just then, he heard a strange noise.
Harry: Hello?
The door creaked open. He could hear a familiar cackle from what was years ago.
Harry: Who's that?
???: Son.
He looked back and in the mirror, he saw…..
Spirit Norman: I'm here.
Harry: Dad? I thought you were…
Spirit Norman: No. I'm alive in you, Harry. Now it's your turn. You swore to make Spider-Man pay. Now make him pay.
Harry: But Pete's my best friend.
Spirit Norman: And I'm your father. You're weak. You were always weak. You'll always be weak until you take control. Now you know the truth about Peter. Be strong, Harry. Avenge me. Avenge me!
Harry: No!
He threw the dagger at the mirror, shattering it into pieces. But it wasn't a mirror, for it was a secret passageway. It led to a secret lab, full of pumpkin bombs, a Green Goblin mask, and a formula that was responsible for his father's insanity. He then saw a glider that was once ridden by his father. Beside it was a letter. Harry picked it up and it read 'Condolences -M. Tweedy. The Purple Lady.' He knew what he had to do now. Peter was Spider-Man, and he must pay for what he did to his father. The next morning, at the catheral, John Jameson was getting ready to be married when a young woman gave him a note. From what he read, it meant that M.J. called it off.
J. Jonah Jameson: Call Deborah.
Mrs. Jameson: The caterer?
J. Jonah Jameson: Tell her not to open the caviar.
Mary Jane was running out of the church and went to look for Peter. In his apartment, he noticed Mary Jane was behind him in her wedding dress.
Mary Jane: Had to do what I had to do.
Peter: Mary Jane.
Mary Jane: Peter. I can't survive without you.
Peter: You shouldn't be here.
Mary Jane: I know you think we can't be together. But can't you respect me enough to let me make my own decision? I know there'll be risks. But I want to face them with you. It's wrong that we should only be half-alive.. ...half of ourselves. I love you. So here I am, standing in your doorway. I've always been standing in your doorway. Isn't it about time somebody saved your life? Well, say something.
Peter: Thank you, Mary Jane Watson.
The two embraced for a kiss now that everything is back to normal.
Buttercup: Hey, why is she kissing my love interest?
Blossom: You didn't know? MJ is Peter's new boyfriend.
Buttercup: (shocked) What?! (Faints)
Bubbles: You ok, Buttercup?
Buttercup: (gets up) I'm good. I'm over him now. Don't know why did i fell in love with him in the first place.
Suddenly, a man appeared.
Vern: I'll tell you why. 'Cause you girls are single and not one boy will ever love you. (Starts dancing and messes up) Damn. Play me off, Johnny.
Johnny starts to play random music on the piano and Vern was dancing.
Blossom: Who are they?
Lincoln: I have no clue.
Bubbles: What do we do?
Lincoln: Just hit them with the hammer.
Buttercup: (gives one more evil smirk) Got it.
Vern: Say what now?
Before anyone can react, Buttercup jumps over in front of Vern and Johnny, then brings her hammer around to collide with the two as they soar straight into the sky like Team Rocket blasting off again.
Buttercup: Man, that's feels good.
In the distance, Peter heard helicopters. Crime was in the air.
Mary Jane: Go get 'em, tiger.
And so, he went off. He has his spider suit repaired again and swung on his web as M.J. looked in the distance. Peter's life was back to the way it is. His girlfriend came back, and now, he's ready to take on crime as Spider-Man forever.