Welcome everyone to the sequel to my first Sonic/Thomas crossover, and while this may have came sooner, I had other stories to work on and I needed to make sure I had all of my ideas written down. Deciding on certain Sonic villains is much harder than I thought, though it will be less than last time. I will go ahead and say that Mephiles from Sonic 06 will be featured in this, however it's not the one from the game, instead another one from an alternate universe, basically the one shown briefly in the archie comes in the Zone Jail.

Listed below are the Arcs for this story:

Arc 1: Sodor Boom Boos

Arc 2: Pirates On Rails

Arc 3: Bio-Island

Arc 4: Titans Of Sodor

Arc 5: Crystalized Darkness

Characters like Lyric, Metal Sonic, King Arthur and the Metarex may re-appear. I want this crossover to be much better than the previous and as you may see, I went a bit bigger.

Reminder that like the previous one, not all villains will be completely in character, and the story will LOOSELY connect with the Sonic games, Sonic X, Sonic Boom or the comics. Some stuff will be altered for the story's sake. Anyways, enjoy!

Sonic Chronicles: Dark Island

ARC 1: Sodor Boom Boos

Chapter 1: King Boom Boo PT 1

It has been a year since many of Sonic the Hedgehog's enemies have invaded the Island of Sodor and peace has been restored to the island. It also had been a year since the engines have seen Sonic and friends at all. But they knew the heroes were out defeating evil and keeping their parts of the world safe. However, after so long, evil would rise again, but it would become more than just a simple invasion. It would effect both Sonic's and Thomas' pasts, presents and futures.

Pumpkin Hill...

Shade the echidna was continuing her travels around the planet alone, several times she has visited Station Square and the Island of Sodor to see her friends. But she never stayed long. One night, she had journeyed towards a mountainous area where she felt shivers go down her spine. All of the mountains had massive pumpkin heads on them with glowing yellow eyes and grins. She looked around at all the many pumpkins and tombstones. She did not feel comfortable.

"Woah, this place is really creepy...hmm...maybe someone lives around here." Shade wondered.

She kept her helmet on hoping she'd intimidate anyone who tried to harm her, it worked many times before. Leaping down a few ledges she found herself having to teleport to different mountains since there were large gaps. She knew if Knuckles was here, he could've just glided around. Her search for anyone turned up hopeless as she stood next to some railroad tracks where a train with a pumpkin face was located.

"That is one creepy train. It's so quiet around here, I guess no one really is around, just the cold." Shade rubbed an arm.

"BLEH!"

Suddenly Shade gets the shock of a lifetime when she is jolted back from a small ghost with large spirally eyes and sharp black teeth and claws jumping into her face and growing before fading away. Shade clutched at her beating chest before pulling out her leech blades.

"GHOSTS? I DON'T HAVE TIME FOR GHOSTS!" Shade growled.

She looked around, the ghost was gone. Thinking she was in the clear, she proceeded to warp to a different mountain, only for 3 ghosts to jumpscare her, but this time she swung her leech blades. The ghosts gasp and fade away just in time.

"Damn...who do these ghosts think they are?" Shade wondered.

She figured they must inhabit this place...and now she needed to get out of here. She suddenly heard laughing from several of them.

"IT ISN'T FUNNY!" Shade spun around trying to find them.

It was at that moment she could sense a ghost trying to sneak up on her, so she shut her eyes and swung a punch and nailed the ghost directly between it's large eyes. Seeing that she made her mark, she chuckled as the ghost rubbed it's face in agony.

"Yeah, didn't see that coming did ya?" Shade teased.

The boo gave her an annoyed look before rolling his eyes. Shade continued to speak.

"Next time you or those boos scare me, I'm destroying all these mountains." Shade threatened.

The Boo looked angered by that and growled. Shade puts away her leech blades and throws up her fists.

"You got something you wanna say you big-eyed creep?" Shade asked.

The Boo curled it's own claws into fists about ready to fight. As the two circled each other, Shade had no idea more boos were started to arrive...and soon was a much bigger one. Shade made the first move by lunging, only for the boo to move to the side and smack her upside the head. Shade turned around and kicked the boo in the face knocking it down. Suddenly she is sucker-punched by another boo, then bit on the arm by a third.

"UGH! GET OFF ME!" Shade demanded.

She grabbed the end of the biting boo and smacked him into the puncher. The first boo recovered and lunged again along with 5 more. Shade shut her eyes, no longer able to look them in the eyes and started to swing wildly with her eyes shut. Realizing she was hitting nothing, she opened her eyes to see the boos laughing at her foolishness.

"STOP LAUGHING AND FIGHT!" Shade demanded.

The boos looked at each other, then started to fuse together and formed into a Boo version of Shade, also with the spirally eyes and sharp teeth, the form was even her height.

"WHAT? HOW DID YOU GUYS...oh nevermind, GO AWAY!"

Shade lunged at her Boo version but the clone grabbed her arm then head-butted her. Before Shade could focus, the clone punched her twice in the head before sweeping her off her feet and laughed.

"Ugh...I'm not through." Shade grumbled.

She warped away and the clone looked around but couldn't find her. Then she appeared behind the clone and tackled it down where the two wrestled around for a minute before they heard a voice.

"STOP!"

The voice caused both to stop, Shade looked towards the direction of the voice to see a very large ghost with blue lips, yellow eyes and sharp claws looking down on them, he didn't look happy.

"Whoa...now that's big." Shade said.

"BOOS ENOUGH! LET HER GO!" He demanded.

The clone whines before splitting into the multiple boos. The large boo, known as King Boom Boo lowered down to Shade who was busy dusting herself off.

"Who are you?" He asked.

"I'm Shade the echidna, I was doing some traveling until your goons here started scaring me." Shade glared at the boos who stuck their tongues out at her.

King Boom Boo glared at his minions who were now ashamed.

"Ugh, we've been over this countless times...we don't scare guests anymore, don;t you remember what happened to the last 3?" King Boom Boo asked.

He looked over at 3 of the tombstones that were lined together, Shade shuttered. Looks like she had more bravery than they ever did. She looked towards the red sky and sighed.

"Well I should be going, I didn't plan on staying longer than I needed to." Shade said.

"HOLD IT GIRL!"

Shade stopped and shook in fright at the King's change of tone. She turned around getting a few giggles from the boos.

"What now?" Shade asked.

"Earlier we felt a strange disturbance around Pumpkin Hill, a few of my minions went to check it out, but they never returned. This place may be big, but it's hard for one of us to not get lost. Think you can help us locate them?" King Boom Boo asked.

Shade scoffed, after scaring and fighting with her, what made him think she was going to help them? Then again, it didn't seem like she could easily escape them, sure she could teleport, but checking her warp belt, she realized it needed to recharge for being used so much recently.

"I guess I have no choice...but how could I possibly find them? All the boos look exactly the same, are any of you even girls?" Shade asked.

Surprisingly, several raised their hands...yet they looked exactly like the others. Dropping the subject, she looked towards several of the nearby mountains for anything out of place. Maybe if she could locate the source of the disturbance, she may find some kind of clue. Before she started, a small explosion shook the ground she was standing on. They all saw some smoke rising from one of the mountains where the large pumpkin at the top was frowning.

"I'll check there!" Shade said.

She saw one of the underground rockets nearby and activated it so she could fly towards the mountain. As she got there...she saw nothing but a large crater where the explosion happened. No boos were around, well until a few seconds later when she's jumpscared again from behind. Shade turned around figuring it was the same Boo who tried to fight with her the first time.

"UGH! GO AWAY! I'M BUSY!" Shade growled.

But the Boo only laughed and pointed at her.

"Such foolishness." Came a voice.

"What?"

Suddenly Shade and the Boo are blinded by a bright light. Shade tried to make out what was causing it, but she only got a glimpse of crystalized spikes before she and the Boo vanished from Pumpkin Hill.

Island of Sodor...

Back on the Island of Sodor, nighttime had rolled around most of the engines were finished with their jobs. At Tidmouth Sheds, most of the engines were already sleeping, everyone except for Henry and Percy who were pulling the Flying Kipper and mail respectively. Unknown to the engines, they had new visitors. As Henry traveled towards the Mainland carrying the Flying Kipper, he looked up at the sky worried.

"Aw...it's going to rain soon, I need to hurry. I mean I'm not scared of the rain anymore...but it would still be nice to remain dry." Henry said.

Suddenly as he went around a bend, he was suddenly jumped by a ghost that faded right through him. Henry screamed and shut his eyes after seeing the large spiral eyes and sharp teeth. He braked hard and all the vans rammed into each other tossing around some of the crates of fish inside. Thankfully this time he didn't derail.

"WHAT WAS THAT?" Henry whimpered.

He was too scared to move on and kept his eyes closed in case it happened again. His driver and fireman looked around confused, they hadn't seen anything. At least until the driver takes another look outside the cab and gets jumped by the ghost as well as it fades away. The driver accidently tackles the fireman down.

"Sorry about that." The driver helped him up.

"No problem, that must have been what Henry saw just now." The Fireman figured.

"GHOSTS! I HATE GHOSTS!" Henry screamed.

While he panicked, the ghost, known as a Boo, was high in the air laughing at them. He wanted to try and possess someone but he needed a better victim. So he left to find someone else. Percy was still delivering the mail but was almost done.

"The sooner I get this done, the sooner I can rest easy." Percy smiled.

He was so used to taking the mail that he wasn't even tired. He knew he was doing the island a great service and that made him happy. Whistling into the night, he attracted the attention of a Boo who followed Percy. The Boo grinned evilly as he got ready to cause some trouble, however his plans were halted when it started to rain. Thunder and lightning boomed and flashed all over the sky and the Boo got scared. They didn't get much of this weather in Pumpkin Hill, not even around Aquatic Mine or Death Chamber. Knowing he needed to get out of the rain, he fazed right through one of the vans and saw the bags of mail.

"Hehehehe..." The boos giggled.

He started to throw the mail all around the van causing such a mess. Then he proceeded to do the same inside the other 2 vans. Every time Percy would stop at a station, the workers at the station would be baffled by the mess and had to sort them all back. This caused Percy to be late to every station left. On the way back to the sheds, Percy was thinking about the mess.

"They were all in the bags, how could they all have scattered around? Hmm...I guess I'll have to make sure they're completely tied up, I got lucky tonight, I know Sir Topham Hatt wouldn't be happy. He'll probably still talk to me in the morning." Percy sighed.

Suddenly, he hears ghostly laughing.

"What? Who is there?" Percy called out.

Suddenly the Boo floated up in front of him with a wicked grin, this scared Percy.

"AAHH! A GHOST!" Percy screamed.

He braked hard as the Boo laughed then went around to cab to scare his driver and fireman. The Boo wanted to do more than just scare them, he then shoved the two men out of the cab where they landed in a bush safely, then the Boo took control. He started to pull random levers and jolt Percy forwards.

"HEY! YOU CAN'T DO THAT!" Percy said.

The Boo ignored his cries and made Percy go faster and faster down the line, he was now considered a runaway. The Boo laughed as he blew on Percy's whistle, Percy could only watch as he raced down the line and around a few bends. He was coming very close to Tidmouth Sheds and saw that the turntable wasn't lined with his track.

"Oh no! HELP! STOP ME!" Percy whailed.

The other engines were awoken by Percy and were shocked to see him coming towards the turntable.

"SLOW DOWN PERCY!" Thomas yelled.

"I CAN'T! I'M BEING CONTROLLED BY A GHOST!" Percy yelled.

"A what?" Edward asked.

Just as the Boo was about to exit the cab, he is suddenly kicked in the face and launched onto the ground. The savior then applied Percy's brakes just in time and Percy stopped with his front wheels dangling above the bottom of the turntable.

"Phew." All the engines said at once.

Then they all turned towards the Boo who hissed at the new figure before fading away. The figure turned out to be Shade who came over to Percy's front.

"Hey Percy, long time no see." Shade smiled.

"Shade! You saved me? Thank you!" Percy said.

"No problem...think you can back up?"

"I can try."

Percy puffed backwards as hard as he could until his front wheels were back on the track, then the turntable turned to line up with his track. The other engines cheered Shade on as the Boo grumbled from nearby. He was then joined by 2 more and they all talked to each other, planning to cause more mischief tomorrow, and also get into contact with King Boom Boo. The Boos were allowed to hang around different parts of the world, as long they talked with King Boom Boo to let them know where they were resided or if the king needed them for something. As Percy went into his shed, Shade sat on his front deck.

"So Shade, what was that ghost? Do you know him?" Percy asked.

"Oh I got some explaining to do." Shade rubbed her head.

She had to remember to contact Sonic and his friends tomorrow...looks like the Island was in danger again. Nearbye, the engines and Boos were being spied on by the figure Shade could barely see, the crystalized menace evilly chuckled.

"This should be interesting...I've heard the stories about this place...and how that irritating blue hedgehog managed to save them countless times...and it included that little blue tank engine. I'll be watching for now...but I will plan a few surprises for them...I'll consider it a test. See you soon Sonic the Hedgehog and you'll meet me soon enough Thomas the Tank Engine."

With that the figure sunk into the ground and out of sight. With the blue blur's help it was time for Thomas to prove again that little engines could do big things.

To be continued...

Next time, Shade will seek the help of Sonic and co. to help capture the Boos, while at the time King Boom Boo gets word of the Island of Sodor and heads there to takeover it. Will his plan succeed or will Sonic have the final scare? STAY TUNED!