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]
[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!
Surge: On it!
Stringer: Way ahead of ya!
Breez: Let's go!
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?
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.
[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?
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?
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?
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?
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]
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?
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.
[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?
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?
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.
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.
Joy: That's it!
[Joy picks up Anger and burns Von]
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?
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?
Nya: [on COMM] What's wrong? Did you fail? Has Yveltal been revived?
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.