Here's how Thomas and Percy's battle goes in Wrath of the Country.
[Soon another Knight comes alive]
Jedi Knight Prime: Protect the staff!
[Soon the soldiers fire as another one appears behind the other knight, but something fires at them and the other knight is killed by a lightsaber and it reveals Thomas!]
Brian: Oh, my God, Thomas.
Twilight: You came back!
Thomas: I come for that staff your holding, Earthling.
[Thomas walks towards]
Thomas: Give me the staff, Twilight.
Twilight: Thomas, what are you talking about? It's me. Twilight!
Thomas: You dare question me?! I fight for my own kind now!
Vinny: This isn't you, Thomas.
Thomas: Give me the staff, Twilight. Or die.
Brian: Twilight, give it to him.
Twilight: What? Brian are you...
Brian: Just give it to him now!
[After a moment, Twilight gives it to Thomas. But Cody fires at Thomas as the others do the same. But Thomas blasts them]
Optimus: Thomas, stop!
[But he grabs him and flips him over]
Thomas: You dare to challenge me?! Well, this world of yours will now be destroyed.
Percy: Something's wrong. That's not Thomas!
Brian: We got to stop him!
Twilight: I'll do it.
Percy: No. I'll do it. He's been my best friend ever since I met him. And I'm the one who should face him.
Optimus: Percy, be careful.
Percy: I will. [draws his energy axe]
Brian: Sylveon, you, Vinny, and Fluttershy, get back to the sub.
Sylveon: What about you?
Brian: We're going after Thomas.
Brian: Just go.
Sylveon: No, I'm not leaving you!
Fluttershy: [grabs her] Sylveon, come on! Get to the sub!
Vinny: Let's go!
Optimus: I'm coming as well.
Captain Rex: Alright, let's head back to the subs! Contact on the top and tell them we lost the weapon.
[The troopers leave but Rex stays behind]
Commander Cody: You heard him back to the sub.
Twilight: Aren't you going with them?
Captain Rex: I'm gonna help you find him.
[They head on. And now, the ship is rising and we see Percy chasing after Thomas as they get knocked down by the sub, as "Decisive Battle on the Ice Field (Rayquaza vs. Deoxys)" begins playing. And now the ship rises out of the water, and Thomas and Percy jump out of the water and Percy swings his axe to hit Thomas' face and slams his head on the ship. And we see Brian, Twilight, and Rex struggling up to get to the top]
Captain Rex: Come on! We got to keep going!
[They are now on the surface]
Brian: Holly shoot! This thing's moving!
Twilight: Look! [points to Thomas and Percy] There they are!
Brian: Come on, let's go!
[They run towards them as the ship is wobbling but then a big wave arrives]
Captain Rex: Watch out! A wave!
[They get splashed down as Brian slides down, but Rex dives in and grabs his hand. It goes back to Thomas and Percy as they clash their lightsabers. And they come into a blade lock]
Percy: Thomas, you got to snap out of it! It's me! Percy! Your best friend!
Thomas: I don't have any friends, Percy! Your not my friend! I am OpThomasis Prime! [grabs his throat] And you are nothing! [throws him]
Percy: Then I shall do what I must. [deploys his face shield]
[We see a battleship nearby the ship and we see jets flying pass]
Pilot #1: Lightning four has visual on OpThomas.
[Brian and Twilight run to Thomas]
Brian: Thomas! Thomas stop it!
[Twilight climbs on top of him]
Twilight: Thomas! Look at me! You can't do this!
[Percy jumps over and hits Thomas' face with his axe. He grabs to axe to shoot Percy, but he misses and Percy kicks him down and was about to hit him again when a wave splashes him down as they slide down, and Percy fist punches Thomas and the ship rises higher, and Brian and Twilight slide down, and Thomas grabs Percy's throat and slams him on the wall and Brian and Twilight slide down towards him, as Thomas it fist punching him, and tries to stab Percy's face but deploys his face shield. But Thomas tears it off ready to strike again]
Brian: Thomas! NO!!!
[When Thomas is about to kill Percy, but something blocks it and it was Willy's lightsaber!]
Willy: Thomas the Tank Engine. It is I, your oldest friend: "William C. Orca". I would lay down my life, if I were you.
[Soon Thomas stops and his eyes to back to normal]
Thomas: Willy. [his scar disappears] Twilight, Brian, Percy. I'm so glad to see you again.
Princess Celestia: Twilight!
Princess Celestia: Thank goodness, your safe.
Brian: Guys. That stuff, we didn't mean it.
Sharky: Hey, don't worry about that. [puts his fin on his back] It's all water under the bridge.
Ed: Good friends can forgive each other, Brian.
Thomas: [drops his sword and gets on his knees] What have I done?
[Then suddenly Megatrain, Alter, and Starsmoke appear and fire a rocket]
Megatrain: Quintessa was the ruler of our Gods! I knew you couldn't do it! [take step staff from Thomas] She knows I'm strong, and your weak!
Alter: You've turned your back on Cybertrain, OpThomas! Now, you will watch your planet die!
[They transform and fly away]
[Just then the other Cybertrain Jedi Knight appear as Clocker, Vinny, Fluttershy, and Sylveon appear]
Clocker: Oh, dear.
Fluttershy: What's wrong?
Clocker: Not doing so well!
[Soon the knights start attacking Thomas]
Cybertrain Knight #1: You betrayed your own kind!
Brian: Thomas! You gotta get up!
Cybertrain Knight #2: You've chosen the wrong side.
Thomas: I can't. There going to kill me.
Twilight: You have to make them stop!
Thomas: No, Twilight. Maybe it's better this way.
Cybertrain Knight #3: Quintessa is the great DECEIVER!!! [slashes Thomas with his sword]
Cybertrain Knight #4: She put you under a spell! [hits him with his axe]
Cybertrain Knight #5: And the sentence is, death!
Twilight: NOOOOOOOO!!!!!!!! (as she screams she starts to glow)
[Just when he's about kill him, the talisman on Brian turns into a sword and he stops him just in time as Brian looks at it impress. As the knights put their swords around him]
Cybertrain Knights: Save us, brave warrior.
Brian: Twilight, look!
[Twilight looks and sees she has her wings!]
Twilight: [gasps] My wings! There back!
Brian: [drops the sword]
Twilight: But, I wanted to be a duchess. I can't be a princess again!
Brian: Maybe that doesn't mean you can't be a princess again. I guess they only react when something big is happening. Like saving the world from Cybertrain!
Twilight: I think your right!
Fluttershy: (with tears in her eyes) Willy. I don't hate you.
Willy: I know, I'm so sorry.
Fluttershy: I'm sorry too. I just wanna be friends again, my friend.
Willy: It's fine now.
[Fluttershy weeps in Willy's chest as he rubs her back, glad to have his friend back]
Thomas: Optimus. I have failed you. Including, Twilight, Brian, and everybody else. Including Earth. I have doomed it. The only planet in the universe where I called it.... "home".
Brian: This wasn't your fault, Thomas. Only you can make it right. We can't do it without you. It's only one moment. It's up to you, without you, will all die. It's now or never.
Thomas: Cybertrain Knights! I will never betray you ever again. I am, OpThomas Prime! In order to save Earth, we must go to Cybertrain, and destroy Quintessa!
Myserious voice: Hey!
[They look up and see the others in Lockdown's ship]
Peter: Don't you guys need a little help? [laughs]
[Everyone looks and Brian and Twilight excitedly smiled]