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This is how Thomas recovers and for the honor of Stormer goes in Thomas and Twilight Go To The Hero Factory.

[We view Thomas lying on the floor. He wakes up and heaves himself up. Our heroes and the Hero Factory Heroes run up to him]

Twilight Sparkle: Thomas!

Percy: Are you okay?

Furno: What happened?

Thomas: [gets up] If you guys want the story, here it is. Stormer sacrificed himself to save me. And now, Meltdown's got both him and Cole.

Everyone else: [gasp]

Pinkie Pie: Which way did they go?

Thomas: [points] That way.

Rainbow Dash: Oh, no.

James: Stormer won't survive out there alone.

Rarity: Don't worry, James, we'll get him and Cole back.

Thomas: No, Rarity. There's no time. We've lost Stormer and Cole and it's all because of me. [clenches his fist]

Percy: Thomas. Don't beat yourself up.

Twilight: Yeah. Don't blame yourself for something you didn't do.

[Twilight looks around]

Percy: Thomas?

[Our heroes rush outside to see Thomas hitching himself to a rope]

Twilight: Thomas, what are you doing?!

Thomas: I'm going after Stormer. I couldn't protect him before so I've gotta help him now.

Surge: But, kid, you can't go out there on your own.

Thomas: What other choices are there, Surge? If anyone should try to help Stormer and Cole, it's me.

Virgil Tracy: But what if you need back-up?

Thomas: Virgil, you have to understand. You aren't coming with me, none of you are. This is now a rescue mission and I am the only one going.

Bumblebee: But, you never know when Meltdown may strike again.

Thomas: If you don't mind being chased by bad guys, shot at, or tortured, then fine.

Ratchet: Thomas, listen to me. If you're going to rescue two of your friends, you're going to need back-up in case we encounter Meltdown again.

Thomas: [sighs] Ratchet, I have to do this alone. Okay? I'm sorry.

Furno: [frowns] Fine. If you wanna walk into a trap just because you're blaming yourself for something you didn't do, then do it.

Optimus Prime: Furno!

Thomas: No, Optimus. Furno's right. I don't want anyone else exposed to Meltdown's spray. [turns to leave but thinks again] [sighs] Who am I kidding? You're right. I do need help if I'm going to rescue them.

Twilight: That's the spirit, Thomas.

Bumblebee: Let's go find Stormer.

Thomas: We can do this. For the honor of Stormer.

Everyone: For the honor of Stormer!

Sari Sumdac: Time to suit up!

Ratchet: Alright, everyone, let's move!

Furno: Gotcha!

Surge: On it!

Stringer: Way ahead of ya!

Breez: Let's go!

Thomas: F.A.B.

Twilight: Let's do this!

Thomas: Hang on, Stormer. We're coming to find you.

[Everyone climbs into Hero pods and take off over Makrohero City]

Surge: Is he down there? Can you see him?

Fixit: I don't think so.

Furno: Wait! I see him! He's racing across the rooftops.

[Everyone looks down to see Stormer racing across the rooftops]

Thomas: Alright, let's go!

Twilight: I don't see why we should follow him, Thom.

Thomas: Come on, Twilight. It's the only way to go after him undetected.

Furno: Thomas is right. Come on, let's go!

[Our heroes quietly follow Stormer]

Stormer: Here are those plans.

Cole: Good job, Stormer. Now let's get back to Meltdown.

Stormer: As you wish.

[Cole climbs up onto Stormer's back and Stormer takes off for Meltdown's lair. Meanwhile, up in the sky, our heroes and the Hero Factory Heroes are looking for Stormer]

Twilight: [frightened] Oh! I hope Stormer and Cole are okay. Wherever they are right now.

Brian: I'm shure they're around here somewhere.

Thomas: Hmm. Optimus, is there a way to get Stormer and Cole back to normal?

Optimus: There might be.

Cheetor: Don't worry. Zib and Quadal are manufacturing an anti-virus right now.

Nyx: We know, Cheetor. But I just hope we can save Stormer and Cole in time.

[Back to Stormer and Cole]

Cole: Okay, we're almost there. Just a few rooftops to go.

Meltdown: [pops up on a hologram] Cole, Stormer, have you retrieved those plans like I asked?

Cole: Yes.

Stormer: There right here, sir. [shows the files]

Meltdown: Good work. Now, get back here before your former friends find you. We wouldn't want to upset our master.

Cole: Indeed. 

[The 3 set off]

[Back with our heroes and the Hero Factory Heroes]

James: [as Spongebob (in his version)] Where can they possibly be?

Rainbow: It's not like we have x-ray eyes, James.

James: I have x-ray goggles.

Pinkie: [gasp] Did Professor Zib give you those?

James: Yeah.

Breez: Zib gave them to us in case we needed them.

Thomas: But still, Stormer and Cole getting infected by those nanobots was all my fault.

Twilight: You can't blame yourself.

Furno: Besides, Stormer and Cole getting infected wasn't because of you, little pal.

Thomas: Thanks, Furno.

Furno: You're welcome.

Twilight: Besides, Thom, Meltdown is the one responsible for infecting people with nanobots and turning them evil. And that's exactly what he did to Cole and Stormer.

Lloyd: We must destroy them quick!

Thomas: Who are you talking about, Lloyd. The nanobots?

Lloyd: Yes!

Thomas: Nya. Have you located Stormer, Cole and Meltdown yet?

Nya: Not yet.

P.I.X.E.L: This must mean that Stormer's blocked his own signal.

Zane: You are probably right, P.I.X.E.L.

[Back with the 3]

Meltdown: [snickers] Von Nebula will be pleased.

[At her lair]

Cole: Von Nebula, ma'me.

Von Nebula: Yes?

Stormer: We have those plans you wanted.

Von Nebula: Very good, Stormer. I am proud with all three of you.

[Meanwhile, not so far away, our heroes and the Hero Factory Heroes are nearing the lair]

Thomas: We're almost there.

Jay: But how are we going to get inside without being seen? They have the place guarded all over.

Thomas: Good one.

Zane: Ratchet, any ideas?

Ratchet: Well, we could try using invisibility cloaks.

Twilight: That's a great idea.

Thomas: Nya, any luck finding Stormer and Cole?

Nya: Negative.

Thomas: Ugh. What's it got to take to unblock Stormer's signal?

Nya: Something's jamming the transmitter.

Thomas: What is it?

Nya: Not sure.

Thomas: How's the anti-virus for the nanobots coming along?

Nya: Neh.

Thomas: What do you mean 'Neh'?

Nya: It means I don't know what it is!

Thomas: Nya! The anti-virus is a virus that counters another's affects.

Nya: Alright, alright!

[Outside, Thunder and Xplode are guarding the entrance]

Xplode: Those Heroes won't know what hit them.

Thunder: Yeah. [laughs]

Rotor: Don't laugh just because he said that.

[Suddenly, Rotor spots something]

Rotor: Look!

Xplode and Thunder: What?

[They see a Hero Pod in the sky]

Xplode: A Hero Pod!

Thunder: Shoot it down, Rotor!

Rotor: Okey-dokey! [does so]

[The blast hits the pod which falls out of the sky]

Xplode: That was too easy!

Rotor: There'll be more soon.

Thunder: And if there are more on the way, we'll be ready for them. [deploys his weapons]

[Meanwhile, our heroes and the Hero Factory Heroes land safely]

Thomas: Let's move.

Bumblebee: But if they spot us, then we're in big trouble.

Rarity: Quite right.

Thomas: We're going to need some kind of distraction. John Tracy, any ideas?

John Tracy: Yes. One of us must make a distraction. And get the files.

Pinkie: I'll do the distraction!

John Tracy: Okay, it doesn't really matter who does the distraction.

[Pinkie marchs in]

Pinkie: Can I have everyone's attention?!

[Everyone turns and looks at Pinkie]

Cole: Something you want?

Pinkie: Yes.

Cole: What is it?

Pinkie: I have to use the bathroom.

Stormer: Oh, it's over there.

Pinkie: Thanks. [goes in]

Peter: Some distraction.

Thomas: Let's just hope they keep their heads turned in that direction long enough.

James: John. What are the files that Stormer stole for?

John: Something to rebuild a weapon system in the desert.

Thomas: What is the weapon called and what is it used for?

John: It's for recreating Yveltal, the Pokemon of destruction.

Thomas: But what is it called?

John: The weapon of "Destruction".

Kai: Then how do we stop them before they rebuild and use it?

John: Get the plans, fast.

Thomas: And how do we do that, fast?

John: I don't know.

Pinkie: [comes back]

Jay: [punches her] Pinkie! You call that a distraction?!

Pinkie: I had to go to the bathroom.

Lloyd: Well, it's not a way to distract evil villians.

Thomas: Let's get those files!

[Back with the 3]

Stormer: Cole and I can't wait to see this Pokemon of Destruction, Meltdown. What does it look like?

Meltdown: It's red with black stripes, and has a Y-like shape.

Cole: And how long is it going to take to rebuild the weapon that is going to recreate it?

Meltdown: We don't know, but it will be born soon.

Stormer: I hear it was destroyed by another Pokemon named Diancie. And the other Legendary Pokemon, Xerneas has restored everything.

Meltdown: Yep. But that's all in the past. Once it's reborn, we'll will be able to revive millions of Decepticons under Von Nebula's command.

Von Nebula: Yes.

Cole: Anyways, when Yveltal is unleashed, nothing will stop us.

Von: Yes!

[Meanwhile, up above them, our heroes and the Hero Factory are watching them. Alan Tracy signals Scott Tracy and points to Von Nebula]

Alan Tracy: Who's that?

Scott Tracy: I'm not sure.

Thomas: That's Von Nebula. I remember her from the show I used to watch. She was once a female hero made by Hero Factory named Von Ness. But she went rogue while on a mission with her former friend Stormer and team leader Thresher.

Alan: Well, then, how did she become a villain.

Thomas: Long story.

Gordon Tracy: Come on. You must know how she became a villian.

John: Gordon, give him time to think about what happened, will ya?

Gordon: Sorry.

Rainbow: Wow! I can't wait to hear this one.

[Back down below]

Cole: Why did you abandon your former teammate and team leader back when you were known as Von Ness, ma'me?

Von: Negative!

Cole: What? Do you mean negative as in 'I don't know what you mean' or negative as in 'I was negative'?

Von: No, terrible idea!

Cole: I'm not giving you suggestions. I'm asking questions.

Von: Oh. I didn't realise. Sorry if I lost my temper.

Cole: That's okay.

Von: Move.

Cole: Yes mam.

[Cole moves away]

Von: Let us begin the sequence.

[Back up above]

Thomas: They're starting!

Joy: [gasp] How are we going to get in?

Percy: Stand back! [blasts the door down]

[Von, Cole, Stormer and Meltdown hear it]

Thomas: It's over!

Cole: How did you find us?

Thommas: Followed you!

Brian: Don't reawake Yveltal, if you do he'll destroy us all.

Von: How come you survived the crash when Rotor shot you down?

Pinkie: Hello? It was decoy.

Anger: Yeah. And besides, robot lady, you need to stop that machine.

Von: Shut it, you tiny red creature.

Anger: I'm an emotion.

Von: I don't care what you are. And I don't care what you say.

Anger: Why, you! [sets a blaze]

Sadness: Anger! Anger! Calm down!

Anger: No! She asked for it!

Thomas: Joy, think of something to calm Anger down!

Joy: Okay. Just give me a minuet to think.

Belle: What?

Joy: That's it!

Thomas: What?

[Joy picks up Anger and burns Von]

Von: AAAAAAAAAAAHHHHHHHHHHH!!!!!

Anger: Now, that's better.

[Von tries to get up and points to our heroes and the Hero Factory Heroes]

Von: Get them!

[The Hero Factory Heroes fight]

Virgil Tracy: Come on, we need to stop that machine!

Disgust: But how?

Virgil Tracy: Follow me!

[Everyone follows Virgil while the Hero Factory Heroes keep Cole, Stormer, Meltdown and Von distracted]

[In the control room]

Thomas: Okay, Virgil. Which buttons turns off that machine?

Virgil: That one!

Thomas: What colour is it?

Virgil: Red.

Thomas: Okay. [preses it but nothing happens] It's not working!

[Then the machines lights up and Yveltal awakens and escapes the facility]

Thomas: We're too late!

Yveltal: ROAR!!!!!!!!!!!!!!!! [flies off]

Alan: Well, at least we tried.

Von: It's over! [leaves while laughing]

Ratchet: We're slagged!

Cole: [to the Nindroids] Lock them up!

[They do so]

Nya: [on COMM] Thomas, what is going on?

Thomas: Nothing.

Nya: [on COMM] What's wrong? Did you fail? Has Yveltal been revived?

Thomas: Yes.

Nya: [on COMM] That's aweful!

Thomas: I'm sorry, Nya. We tried our best.

[They are all thrown in jail]

Stormer: Sorry it had to be this way.

Cole: Don't worry. Things will be back to normal. [sneers] The way Von Nebula wants them to be.

[the 2 leave while laughing]

Sadness: Well, at least we tried.

[Thomas starts to produce tears]

Thomas: What have we done?

Sadness: Thomas, don't feel bad.

Thomas: Sadness, don't bother me. We've lost one too many times already.

Sadness: It's alright.

Joy: Besides, think about how great it will be when it's all over.

Thomas: Alright.

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