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This is the scene for Tirek's request and where Thomas is seemingly killed in Thomas' Place as a Prime

Thomas: I'm listening.

Tirek: Give me and Ernie the Matrix, Blue Ruby, and the Black Pearl. And I'll let you live to be my personal train.

Ernie: Or lose your pals.

Thomas: [looks to his friends for an ideas]

Percy: Don't do it.

Toby: Thomas, don't listen to him.

Rainbow: Don't do it!

Applejack: Yer' our friend T!

Princess Celestia: Listen to Optimus' advice!

Twilight: THOMAS, PLEASE DON'T DO IT!!!!

Ernie: Shut your mouth! [shots lightning out]

Thomas: [thinks for a minute]

Optimus: [in Thomas' mind] Listen to me Thomas, do not let Tirek have the Matrix or the gems for anything! Ever if it means making a sacrifice.

Ernie: What is it going to be, Thomas?

Thomas: NO!! I'M NEVER LETTING YOU HAVE THEM!!! Optimus Prime has taught me a lot of things, but if there is anything he taught me; he's taught me the code of the Primes. As a Prime it is my duty to protect others ever if it means making a sacrifice. Besides, a good Prime puts his friends' lives before his own, and as a Prime I'm willing to do that. If it means losing my life, then so be it.

Brian: That was the best speech I ever heard.

Tirek: [in Megatron's voice] Oh, so unwise. [he readies a blast in his horns]

Thomas: [closes his eyes, ready to accept what's coming to him]

Twilight: THOMAS?!

Brian: Oh, my God!

Vanellope: No, no. No, no, no, no! NO!! NO, PLEASE TIREK!!!

Ernie: Kill him!

Tirek: [fires his blast and it hits Thomas]

Edd: Good lord!

Eddy: AAH!!

Vanellope: NOOOOO!!

Princess Celestia: Thomas!

Princess Luna: No!

[after the dust clears, there is no sign of Thomas]

Brian: [as Frodo] NOOOOOOOOOOOOOO!!!!!!!!!!!!!!!!

Ed: GASP!! THAT MUTANT VAPORIZED THOMAS!!

Twilight: [her eyes start tearing up then she starts crying]

Vanellope: [crying] You really are a jerkinator. [continues crying]

Tirek: That's right, glitch.

Ernie: [chuckles] He's gone. Sorry for your boyfriend, Twilight. He's history.

Twilight: No, no. [falls to her knees]

Vinny: [pulls out his shotgun] Kill him! [he starts shooting Tirek]

Tirek: AAAHHHH!!! YOUR CRAZY MUTT!!!

VInny: YOU KILLED THOMAS!!

Ernie: Yeah, that's the point, where evil.

Brian: [looks a the crater] He's really gone this time!

Peter: I don't believe it!

Twilight: Now I lost the one true thing I love most of all!! No, no. NOOOOOOOOOOOOOOOOOOOO!!!!!!!!!![cries loudly over the loss of her tank engine]

Brian: We just lost a great friend. [a tear streams down his cheek]

Mucker: Yeah, but you just destroyed your keys to getting the army of Deceptitrains.

Tirek: I don't care, I'm am still powerful enough to take over the world!

Ernie: And me as well!

[they cackle then they all hear a blast]

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