Here's how Spencer helps the others in Thomas' Place as a Prime.

Twilight: [crying]

Princess Celestia: [has her student in a hug]

Twilight: I can't believe it! Thomas is gone, Spencer's gone bad. Now the world's doomed! [resumes crying]

Princess Celestia: I know, we must stop him ourselves!

Steam Mech: [knocks on Celestia's head gently] Hello! Is anyone home?! Only a Train-Prime can Defeat Megatrain!

Peter: We have to try!

Steam Mech: But how? We don't have Thomas!

Sylveon: Shouldn't we try to get to a shelter?

Brian: No. It wouldn't matter.

[Then they heard Spencer's whistle]

Spencer: Guys!

Princess Luna: Hmm?

Spencer: Guys!

Wreck-it Ralph: YOU!

Spencer: Hey, wait it's not what you think.

Twilight: What do you want? You have another evil insult to throw at us?

Spencer: Megatrain, tricked me! He lied to me about us being partners.

Fluttershy: So, Megatrain pulled a trick on you?

Spencer: Yes.

Twilight: [shedding tears] What does it matter now?! THOMAS IS GONE!!! AND THERE IS NO WAY WE CAN STOP MEGATRAIN!!

Brian: We're all out of ideas!

Spongebob: [looks in the crater] LOOK! HE'S SAFE!!

Twilight: No, Thomas is not safe Spongebob! HE'S GONE!!!!

SpongeBob: No, really guys, He's safe! He's safe! He's safe! Sa-a-a-fe!!!

Squidward: Will you cut that out?!!

SpongeBob: [to a conga beat] Safe, safe, safe, safe! Safe, safe, safe, safe, safe, safe, safe, safe, safe! [rips himself apart then the two parts go in circles and then they connect again. SpongeBob starts doing a conga dance] Safe, safe, safe, safe, safe, safe, safe, safe, safe, safe, safe, safe, safe, safe, safe, safe, safe! Safe, yes he is safe!

Edd: Sponge, what are you talking about?

SpongeBob: Look in the crater!

[everyone looks down in the crater]

Edd: No, it can't be!

[we view the inside of the crater and see Thomas is perfectly unharmed]

Thomas: Huh? [looks up]

Spongebob: Thomas is fine! [starts crying happily] He's safe! SAFE! [jumps down the crater only to hit something and bounce back]

Applejack: What in tarnation?

Thomas: I'm okay!

James: [stutters] HOW?!

Mucker: Wait a Minute. [drops a tiny stone and it bounces back]

Edd: The Matrix and the gems must've put a shield over Thomas before Tirek's blast hit him.

Sergeant Calhoun: D's, correct!


Thomas: [comes out of the crater]

Twilight: [kisses Thomas] You came back!

Thomas: I was never gone, I was in the crater the whole time. 

Spencer: I know where Megatrain's machine is!

Princess Celestia: You do?

Spencer: Yeah, it's inside the tallest mountain just beyond here!

Princess Luna: We must stop Megatrain!

Thomas: But I'm not a robot.

[then a beam comes down from the sky]

Eugene Krabs: Oh no, is there another evil guy comin'?

Brian: Hit the dirt!

[The beam hits]