Here is a revised version of Season 1 of Yu-Gi-Oh! The Sodor Chronicles with more mistakes fixed and new things added in. The original version of the story was originally posted on the account of Jriddle41, but it's gonna be moved to my account. The story was done in collaboration between me and Jriddle41 (Sodormatchmaker on DeviantART), and we both own the OCs that are used in the story. Everything else belongs to their respective owners:

Thomas and Friends (c) Hit Entertainment and Mattel

The Railway Series (c) Rev Wilbert Awdry

Yu-Gi-Oh! (c) Konami

Song used in Intro and Outro (c) Unknown

WARNING: Again, the story is rated T (13-plus) for moments of violence and some suggestive themes. Viewer discretion may be advised.

Opening up, Thomas was in the middle of a duel against Commander Laura, one of Sailor John's most trusted pirate commanders, to determine if Thomas and Emily are both safe, or if Thomas is forced to join Sailor John's band, and Emily takes a swim with the fishes in the bottom of the ocean:
-Thomas (LP: 3000) had no monsters on his field, with his Arcana Knight Joker being destroyed recently.
-Commander Laura (LP: 200) had Regina - Princess of Reptiles on her side of the field, and she had just declared an attack with her monster, which resulted in the Arcana Knight Joker being defeated.

"Thomas is in deep trouble." Percy commented.

"Indeed." agreed Edward. "He just lost a powerful monster to one of Laura's. And unless he keeps duelling, we'll lose Emily too."

Discord kept his arms folded and watched on in his thoughts.

"Now that I've seen what cards this lady plays, I seem to recall someone of her kind working with reptiles when I heard about an accident at her lab in Seattle..."

He started to have a flashback...

FLASHBACK

It was three years ago, within the city of Seattle - Washington. Professor Laura was a reptile specialist at a college, and a kind, caring soul. She was well loved by her students and treated the lizards she tended to as if they were her own children. But one day, there was a disaster... The college Professor Laura was working at had caught on fire. The students, teachers. and all of reptiles were evacuated quickly. However, when the fire was put out, Professor Laura was blamed for seemingly causing the fire, and as a result lost her job and reputation.

This unfortunately drove her mad and she disappeared one day, taking the reptiles with her.

END FLASHBACK

The flashback ended, yet Discord still remained in his thoughts.

"I'm guessing that was when she met Sailor John, and agreed to work for him in trying to discover the secrets to those Egyptian carvings."

Back at the duel, Commander Laura's turn was not over yet.

"Since my princess just attacked, her next ability will activate." she stated. "If she had attacked another monster or did a direct attack on the opposing player while her attack is buffed up, she is automatically destroyed!"

Regina - Princess of Reptiles sudden shattered into pieces.

"Phew!" sighed Henry. "That's one less thing Thomas has to worry about."

But Commander Laura still held up a card in her right hand. "Not before I place this card facedown." She slotted it into her Duel Disk.

On cue, a facedown card appeared.

"Go ahead, darling. It's your turn."

Up until now, Emily had remained as quiet as possible. But seeing Commander Laura flirt with Thomas was too much.

"Flirt with someone your own age, you reptile loving floozy!" she shouted angrily.

Thomas just looked firmly at Commander Laura before drawing his next card.

Title: The Reptile Queen, Part 2

"Alright, you!" The blue-haired boy announced. "Look out!"

Turn Five: Thomas Billinton (LP: 3000)
Deck: (33)
Current Hand (3): Exchange, Soul Rope, and Gamma The Magnet Warrior

Noticing what he drew, Thomas took it from his hand immediately.

"I call forth Gamma The Magnet Warrior in attack mode!" Thomas declared, laying the monster card onto a monster field slot on his Duel Disk.

Appearing before them was the pink-colored machine rock monster, posing for battle (Level: 4/ATK: 1500/DEF: 1800).

"Alright!" cheered James. "One direct attack and he'll win!"

"This is where it ends!" declared Thomas. "Gamma the Magnet Warrior, attack Laura directly!"

Gamma obeyed and lunged forth. Commander Laura, however, held up her right hand (showing the palm).

"I'm afraid you've triggered my Trap card!" she chuckled.

Thomas cringed.

"Now go!" As Commander Laura said this, her facedown card flipped face-up and revealed itself. "Lizard Tribe(!)!"

All of a sudden, appearing on the field in defense mode was a half-woman/half snake (Level: 5/ATK: 0/DEF: 2000).

"Where the heck did that come from?" asked Percy.

"That's the effect of Lizard Tribe." explained Discord. "When Laura suffers a direct attack, she can activate that card and special summon in defense mode a level 5 or 6 reptile monster from her hand."

"That's correct!" Commander Laura nodded. "And the beauty part...is that Thomas's attack MUST continue!"

True to her words, Gamma continued his charge and collided his fist with the snake woman. Unfortunately, the female monster merely hissed and pushed the Magnet Warrior back onto Thomas's field, while the failed attack also caused the blue-haired boy to take some life point damage (LP: 2500).

"You walked right into that one!" laughed Commander Laura. "I'm not one to be taken lightly."

Thomas just glared at Commander Laura as he took a card from his hand.

"I place one card facedown and end my turn." The blue-haired boy said, placing the card in a Spell/Trap Slot on his Duel Disk.

A facedown card appeared behind Gamma.

"It's my turn!" said Laura, drawing as she gave Thomas a wink.

Emily saw that wink and seethed, but decided not to say anything about it...yet.

Turn Six: Laura (LP: 200)
Deck: (32)
Current Hand (6): Lagula - Prince of Reptiles, Heavy Storm, Monster Reincarnation, Card Ejector, and Spell Scepter(!)

In an instant, Commander Laura brought her right hand to her monster card on her Duel Disk, changing it from defense mode into attack mode.

"I change my Queen Serpentine into attack mode!" she declared.

Queen Serpentine stood up and towered over Gamma and Thomas both.

"What's she doing?" asked Gordon. "Her monster has 0 attack points!"

Before long, Laura slotted another card into a Spell/Trap slot on her Duel Disk.

"Now I equip my Queen with Spell Scepter!"

A large scepter appeared in Queen Serpentine.

"What this does-" Commander Laura started to explain. "-is give my monster an extra 1000 extra attack points."

Queen Serpentine grew stronger (ATK: 0 - 1000).

"But now, by discarding as many Spell cards I'm holding in my hand to the graveyard, my monster will receive an additional 500 attack points!"

She took two cards from her hand and held them out, showing them to be Heavy Storm and Monster Reincarnation.

The scepter glowed as Queen Serpentine grew even stronger (ATK: 1000 - 1500 - 2000).

"Now, my Queen!" commanded Commander Laura. "Attack his Magnet Warrior!"

Queen Serpentine obeyed and charged a blast from her scepter, firing a magical blast from it. Gamma was hit by the blast and instantly destroyed. Thomas grimaced, but smiled either way (LP: 2000).

"I activate my Trap card!" he announced, poking a button on his Duel Disk. "Soul Rope!'

The facedown Trap card rose face-up and revealed itself.

"Since you've destroyed my monster in battle-" Thomas explained (LP: 1000). "-I can give up 1000 life points and summon a level 4 monster in its place."

Appearing on the field in attack mode was a yellow colored monster with magnets sticking out of parts of its body (Level: 4/ATK: 1700/DEF: 1600).

"And the monster I choose is Beta The Magnet Warrior!"

"Impressive trade in." said Commander Laura. "But that little Magnet Warrior is no match for my Queen."

"Perhaps." Thomas replied. "But weak monsters can sometimes hold great powers."

Commander Laura scoffed, but remained smiling. "I'll end my turn. Your move, cutie."

"Why don't you just set Emily free now?" asked Thomas, ignoring the 'cutie' comment. "Then we could finish this duel with honor."

This only caused Commander Laura to laugh again.

"Honor?" she said mockingly. "Why duel with honor, when I could put life in danger?" The female pirate commander then narrowed her eyes with an angry scowl. "Not after I lost everything!"

"Lost everything?" asked Percy. "What does that mean?"

"So then it's true." Discord said aloud. "You ARE the same Laura who lost her job from a fire at one of the colleges in Seattle."

Reluctantly, the female pirate commander turned to face the creator of Duel Monsters and nodded.

"Yes. It's true. I was that former professor from three years ago."

"Why are you in league with Sailor John?" demanded Thomas.

"Not long after I was fired for that false charge-" explained Commander Laura. "-I ran away and took up shelter in a cave off the coast of New Orleans.

A flashback began...

FLASHBACK

In a cave off the coast somewhere in New Orleans - Louisiana, the former Professor Laura had taken up shelter with her group of reptiles.

"My reptiles were the only friends I had left," Present Day-Laura explained. "The only ones I could call family. I felt like I would be stuck as an outcast forever. But then one day, I met him... Sailor John."

Inside the cave, Laura was sitting by a wall looking very sad. That was she heard footsteps and looked up, seeing a man (Sailor John) walking into the cave.

"W-Who are you?" Laura asked, sounding surprised as Sailor John approached her.

Sailor John merely chuckled in response.

"Let's just say...I'm a friend." he replied. "And I've heard about what happened to you. It would seem you were shunned after what happened at that college, am I right?"

"Yes..." said Laura. "Those...people fired me for a crime I didn't commit!"

Sailor John seemed to fake surprise (not that the former college professor) from hearing that.

"Oh my!" he gasped. "That's awful! It must have left you so broken."

"It did." said Laura sadly. Her sadness quickly turned into anger. "I know why I was fired... They were just jealous of me because I got along with the students better than they could! They must have set me up!"

"Then it would seem that you and I are alike." Sailor John said sympathetically.

Laura quickly halted her rant and turned to face the pirate captain in shock.

"What?"

"We are both considered to be enemies by people who are jealous of us." explained Sailor John. "I myself am on a goal to discover mystical secrets that my former friend told me not to. He was jealous that I was bold enough to go out and make the impossible possible. If you join me, perhaps I could help you get revenge on those fools." He held out his hand. "Do we have a deal?"

Laura stared into that man's eyes for any signs of him lying...but she found nothing but the honest truth. After giving her thoughts a moment to think it over, the former college professor smiled and accepted the hand.

"I accept your offer."

"Ever since then-" Present Day-Laura narrated. "-we've sailed the open seas of the world, gathering allies to search for possible answers to the carvings, and to get revenge on the people who wronged us in any way."

END FLASHBACK

The flashback ended, as Commander Laura continued to speak.

"So you see-" she continued. "-it's nothing personal against you lot." The look on the female pirate commander's face turned crazed once again. "...I'm just following my orders! To ruin this tournament, destroy Discord J. Crawford's reputation, and recruit new members to Sailor John's cause! And I will silence anyone who gets in the way of that goal!"

With that said, Commaner Laura pointed towards the chained up Emily again.

"Like her!"

"Let Emily go!" demanded Thomas. "It's not too late to stop this madness!"

"I'm afraid I can't do that." Commander Laura replied. "If I were to set her free, then it would ruin our little duel. And no offense, but you could do so much better."

"What's that supposed to mean?" asked Emily, sounding insulted.

Not losing her crazed look, Laura only giggled malevolently.

"Oh, nothing. Just make your move, little boy!"

Thomas stared defiantly, but drew his card.

Turn Seven: Thomas Billinton (LP: 1000)
Deck: (31)
Current Hand (2): Exchange and Graceful Charity

The blue-haired boy hook his drawn card and held it out for everyone to see.

"From my hand-" stated Thomas. "-I play Graceful Charity."

Raindrops gently fluttered above him and onto his deck, like celestial light of a sort. The life point gauge started flashing the words 'DRAW' five times.

"This lets me draw three cards, and then I must discard two." explained Thomas, as he drew his three cards. They were revealed to be Alpha The Magnet Warrior, Valkyrion the Magna Warrior, and Magic Jammer. Thinking his next move carefully, the blue-haired boy selected to discard Magic Jammer and Exchange.

"Next I summon Alpha The Magnet Warrior in defense mode!" he announced, placing a card onto a monster field slot on his Duel Disk, sideways.

A green hued machine-looking monster (also with some magnets sticking out of its body) wielding a sword and shield appeared on Thomas's field, but was kneeling in a defensive stance (Level: 4/ATK: 1400/DEF: 1700).

"Also-" Thomas continued, switching the other monster card on a monster field slot sideways. "-I switch Beta The Magnet Warrior into defense mode."

Beta then knelt into a defending position.

"I'm afraid that's all I can do for now." Thomas said, ending his turn.

"Would it really be a bad thing to join us?" asked Commander Laura innocently. "I mean think of the benefits for doing so. You'll be able to sail the wide open seas, helping to unlock many of the world's greatest secrets. And best of all-" The female pirate commander then turned on the charm, wiggling the hips of her shapely body in a seducing manner. "-you can gaze upon my beauty every single minute." She finally flipped her hair a bit before fluttering her eyes. "Who knows? I could even make you my second-in-command."

Emily, despite being in grave danger, was getting really ticked off watching that ruthless pirate hit on Thomas (who was only 15-years old).

"Alright, that's it!" she shouted. "I've had just about enough of you, toots. Thomas doesn't like you and he never will! GET IT THROUGH YOUR THICK-HEADED SKULL ALREADY!"

Angrily, Commander Laura looked over to the captive dark green-haird girl with a dangerous look on her face.

"Unless you want to take a long swim with the fish now, I'd suggest that you shut your mouth now, you little brat!" The female commander warned.

Emily growled as she stopped talking. Satisfied, Laura brought her right hand to her deck.

"That's so much better." She the drew her card.

Turn Eight: Laura (LP: 200)
Deck: (31)
Current Hand (6): Lagula - Prince of Reptiles, Card Ejector, and Reptilian Drain(!)

Looking at her card, the female commander smiled and looked to Thomas.

"I may be down to 200 life points, but that will change pretty quickly, little boy." she stated.

"What do you mean by that?" asked Thomas.

Commander Laura decided to answer that question, and held out her drawn card

"I'll show you." she stated. "By playing this Spell card - Reptilian Drain!"

Upon saying that, Commander Laura slid the card into her Duel Disk, causing the mentioned Spell card to materialize in front of her. The female pirate commander's crazed look had returned.

"Here's how it works; I must control a reptile-type monster on my side of the field, and have at least one reptile-type monster in my graveyard. If I meet both of those conditions, then I can go ahead and banish as many Spell and Trap cards that I have from my graveyard. For every card that I do banish, I'll gain 500 life points!"

"Since she has three-" said Edward grimly. "-that means she gains 1500 life points."

"Correct!" laughed Commander Laura. "But it won't be 1500 life points I'll gain!"

"What do you mean?" asked Thomas.

"It's quite simple." The female pirate commander went on. "It's all thanks to my Reptilian Drain's secondary effect! If I have an equipment Spell card attached to any of my Reptile monsters, i can tribute that card and double the amount of life points I gain!"

Queen Serpentine's Spell Scepter instantly vanished.

"With Spell Scepter sent to my graveyard, I now gain 3000 life points!" Commander Laura cackled, gaining a huge amount of life points (LP: 3200).

"She's almost back to 4000 life points!" cried James.

"But she made a huge mistake." said Toby. "Without that Scepter, her Queen's life points go back to 0."

"Did I?" Commander Laura smirked. "Just remember, I haven't actually declared an attack yet. So I'll go ahead and switch my Queen Serpentine to defense mode."

Queen Serpentine started kneeling down in a defensive stance (DEF: 2000).

"That's all for me." The female pirate commander said simply. "Your move."

Thomas was stuck in his thoughts... "She's a good duelist. The way she withstood my Arcana Knight Joker's attack, managing to destroy it, and now recovering almost all her life points. But I won't give up. Not when Emily is counting on me."

He finally drew his card.

Turn Nine: Thomas Billinton (LP: 1000)
Deck: (27)
Current Hand (2): Valkyrion the Magna Warrior and Monster Reborn

Thinking on his move carefully, Thomas slotted Monster Reborn into his Duel Disk.

"I play the Spell card Monster Reborn!"

The mentioned Spell card materialized face-up.

"With this, I can bring back a monster from my graveyard." explained Thomas. "And I choose Gamma The Magnet Warrior!"

Gamma The Magnet Warrior reappeared onto Thomas's side of the field, joining Alpha and Beta.

"Why would you summon that weakling?" Commander Laura demanded. "It's useless right now!" But then she realized something... "Unless..."

"Now that Alpha, Beta, and Gamma are together on the field-" announced Thomas. "-I can use them to create something more powerful!"

The three Magnet Warriors came apart into many pieces. With that, the pieces of the three monsters rose into the sky and combined together in a ball of light. When the light dimmed, there was the monster that the magnet pieces combined into. It was a fusion of the pieces belonging to Alpha, Beta, and Gamma, and its weapon was the same sword Alpha used (Level: 8/ATK: 3500/DEF: 3850).

"Behold, Valkyrion the Magna Warrior!" cried Thomas.

The Tidmouth Teens gazed in amazement at the new monster.

"Whoa..." Henry gawked. "That thing is powerful."

"Weaker than Arcana Knight Joker, but still definitely powerful." James added.

Discord only kept his neutral expression.

"Valkyrion-" commanded Thomas. "-attack Laura's Queen Serpentine!"

Valkyrion the Magna Warrior obeyed and charged and slashing its sword into Queen Serpentine, destroying her in a single blow. But because she was in defense mode, Laura took no damage.

"I'll end my turn."

Emily continued to watch the duel, hoping that Thomas can win and save her and himself from these pirates.

"Come on, Thomas." she thought to herself. "You can do it..."

"It's my turn!" announced Commander Laura, drawing a card.

Turn Ten: Laura (LP: 3200)
Deck: (30)
Current Hand (3): Lagula - Prince of Reptiles, Card Ejector, and Pot of Greed

Smiling to herself, she slotted her drawn Spell card into her Duel Disk.

"I'll play Pot of Greed! Now I draw two extra cards from my deck!" The female pirate commander drew two more cards. They were shown to be the Ritual Spell card Lizard Lagoon Ritual(!) and the ritual monster Escargoon - King of Lizards(!). "Next I activate the Spell card Lizard Lagoon Ritual!"

The mentioned Spell card instantly materialized face-up. Appearing out of the spell was a large pool of ooze between two large torches.

"To work this ritual, I must offer monsters from my field or hand until they have a combined level of nine or higher." Commander Laura explained, before taking and holding out the two remaining monster cards from her hand (Lagula - Prince of Reptiles, Card Ejector) "And I'll offer these two monsters as my sacrifices."

The two monsters appeared onto the field. One looked like a half man/half snake. The other looked like a small child dressed similarly to Dark Magician Girl but with different colors. The two were then sucked into the ooze. The remaining Tidmouth Teens (and Mavis) all didn't like where this was going.

"I don't like the looks of this, guys." Percy gulped.

"Me neither." agreed James.

After a few seconds, the torched burned black flames as a beam of purple light shot out from the ooze.

"The ritual has commenced!" declared Commander Laura, holding out her monster card. "Come forth, Escargoon - King of Lizards!"

The beam of purple light touched the sky, as the female pirate commander began to chant a...well, summon chant.

"Great king of the reptiles, heed my call. Rise from your murky lair and vanquish my foe! Ritual Summon!" Commander Laura chanted.

The darkened clouds spout lightning for a few seconds before another beam of purple light shot out, this time towards the ground on Commander Laura's side of the field. While this happened, the female pirate commander continued her chant.

"Appear now!" she called, slapping the monster card onto her monster zone. "Ruler of all reptiles: Escargoon - King of Lizards!"

The purple beam dimmed, revealing a VERY monstrous looking lizard twice the size of Valkyrion the Magna Warrior. It had razor sharp teeth, sword-like claws, and beady-but-hungry looking eyes. Needless to say, the crowd was terrified beyond belief.

"Man, that's one big lizard." Percy gulped, staring in awe and fear.

"You said it." shivered Henry.

Commander Laura was laughing psychotically. "You're all done, little boy. My Lizard King is going to finish you here and now."

Escargoon - King of Lizards merely growled in agreement (Level: 9/ATK: 3500/DEF: 2000).

"He's got the same attack as Valkyrion!" objected Thomas. "If you attack, they'll destroy each other."

On cue, Commander Laura's crazed look returned. "Oh, I think not." she remarked dementedly. "By sending one reptile-type monster from my deck to the graveyard, my monster will not be destroyed by battle."

As she explained her monster's effect, a card slipped out from her deck and Laura sent it to her graveyard.

"In order for my monster to attack also, I must pay half my life points." Commander Laura continued, as her life points halved down (LP: 1600).

"That can't be good." muttered James.

"Now go, my Lizard King!" shouted Commander Laura. "Destroy Valkyrion with Toxic Swamp Breath!"

The giant lizard obeyed, letting loose a huge belch that summoned a cloud of odour. Valkyrion tried to fight back, but was unable to do so and got destroyed as a result.

"Valkyrion!" called Thomas. Thankfully, his life points were untouched.

"This is awful." Toby commented. "That was Thomas's most powerful monster."

"We have to keep believing in him!" protested Edward.

"Agreed." Discord nodded. "While it's true that Valkyrion was Thomas's best monster so far, there's still a chance that he can pull a comeback trick. The question is...will he do it soon?"

"Got that right, Discord." agreed Gordon. "That lizard is more than powerful enough to finish Thomas off if that pirate gets the chance."

Emily, meanwhile, was still observing the duel from the very high height and was more worried than ever for her blue-haired friend.

"Thomas..." she thought quietly.

"With that, I end my turn." said Commander Laura. "Now make your final move."

Thomas sweated and drew his card, looking at it long and hard.

Turn Eleven: Thomas Billinton (LP: 1000)
Deck: (26)
Current Hand (1): Pot of Greed

"This is awful." he thought to himself, unhappy with what he drew. "But I can't give up. Not when Emily is counting on me to save her." Thomas held up his card. "I play my copy of Pot of Greed!"

He drew two cards from his deck. Thomas now had Magical Hats and Dark Magic Curtain in his hand.

"I'm in a tight spot." he said aloud. "But no matter what, I'll keep duelling till the very end."

Thomas then heard laughter coming from Commander Laura, causing him to look up and forth.

"You were a fool to have ever accepted my challenge!" Commander Laura said cruelly, once again having that crazed look on her face. "Once this duel is all over and done, then not only will you have joined our ranks, but you and your friends over there will never see your girlfriend, Emily, ever again! It's over for you! Nothing can save you from my reptiles now!"

Again, the female pirate commander erupted into psychotic laughter.

To be Continued!