The next morning, James and Jen started towards the Ruins of Alph, while Hunter continued south toward the Union Cave. Many of the Pokémon that lived in the area were active, but neither youngster wanted to delay their visit to the Ruins with a drawn-out capture attempt. Cyndaquil was disappointed by this; he wasn't happy about not battling Hunter the day before, and was becoming restless. James let the Fire-type run through the grass along the way, which allowed him to release his pent-up energy.

As the Ruins hove into view, Cyndaquil returned to James' shoulder, and they walked through the entrance gate to see a set of stone buildings, each with strange symbols marking their entrances. Neither James nor Jen could make sense of the ancient script, though.

“What do you think it says?” James asked. Jen shrugged.

“You're guess is as good as mine.” she answered. She spotted a bystander walking their way, and she waved to him. “Um, sorry to bother you, sir, but do you know anyone who can read these symbols?”

"Unfortunately, I don't," the man said. "I think some of the scientists here know how, but I don't know if the research building has opened for the day yet."

"Okay. Thanks anyway," Jen replied, and she turned to James. "What now?"

"Well, we can't just stand around here all day. Let's go into this building here, it can't hurt." Jen nodded, and the pair entered the nearest building.

Inside, a small table sat in the center of a small chamber, with what looked like a sliding puzzle on it. Next to it, a small plaque bore a description of a round-shaped Pokémon that had only been found as a fossil. The two youngsters looked at each other, perplexed, then James spoke at last.

"Go for it, Jen. I think visitors are supposed to try and solve the puzzle." Cyndaquil squeaked an affirmative, and Jen turned to the puzzle, trying to place the tiles in the correct slots. James and Cyndaquil looked on, occasionally trying to help. After about ten minutes, the puzzle was finished. The finished picture looked something like a horseshoe crab with claw-like legs poking out from the front end of its shell. Before James could get his Pokédex out to scan the picture, there ground shuddered, and then, incredibly, the floor dropped into a dark alcove below the building. Both youngsters shouted in surprise, and the now-platform crashed down into what looked like a series of hallways. Fortunately, both of them were unhurt, but neither spoke, too frightened to do so.

"What in the world was that?" Jen asked after about a minute, her voice shaking. "If I'd known the puzzle would do that, I'd have left it where it was!"

"I think the completed puzzle triggered some kind of booby trap," James answered, checking to see if Cyndaquil was alright. Thankfully, the echidna had also escaped harm, but his back was aflame and his posture defensive. "The real question is, where are we now?"

"I don't know, but it looks like the walls have similar symbols to the one on that building we just got dropped out of. I can't make heads or tails of it."

"Maybe it's a secret code?" James asked, examining the walls himself. The symbols had the look of a character system in some archaic language. As he tried to make sense of them, he heard Jen scream behind him. "Jen! What happened?"

"One of the symbols just moved!" Jen shouted, backing away in fear. "James, I think we have to get out of here!"

"Yeah, but which way is out?" James was starting to panic. First the floor dropped out from under them, then moving symbols, what next? As he tried to figure out a plan, he saw a dark shape move towards Jen.

"Hey! Get away from her!" Cyndaquil was off James' shoulder in an instant, and he launched a single fire bolt in Jen's general direction. Jen ducked, and the bolt made contact, knocking the shape backward. All around them, symbols were detaching from the walls and forming a ring around the youngster. Cyndaquil fired his Ember attack at the floating symbols, sending them backward and eventually dispersing them. As they faded into the darkness, James heard a voice calling from the far end of the hallway.

"Hey! Are you kids alright?" Two men were running down the hallway towards them. James recognized one of them as the tourist they had spoken to earlier. The other was a young-looking man in a lab coat, his face framed with concern.

"We're fine, now," Jen answered, getting up from the floor. The whole experience had scared her more than she was willing to admit. "How did you know we were down here?"

"We heard shouts from the first puzzle building. This hallway is the main part of the Ruins; the puzzle structure must be connected to this building."

"Yeah, we figured that out as well," James told him, wary of anything coming out of the darkness. "Thanks for coming to find us."

"Not a problem; it's part of our job to make sure exploration of the Ruins is safe for everyone. Why don't you come back to the research station so we can find out exactly what's happened here?"

"Sounds good. The sooner we get out of here, the happier I'll be." Jen's answer was enough for the researcher, and they followed him out of the building.

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"So, you say the symbols moved when you landed in that hallway?" the researcher asked, writing down the relevant details on a notepad.

"Yes. We couldn't read them, but they seemed to form an alphabet of sorts," James answered. "Jen was the first to notice that they were moving, and then they started coming out of the walls."

"They didn't try to hurt us, though," Jen added, calmer now that they were out of danger. "They just formed a circle around us, and then Cyndaquil drove them off."

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"I think you kids stumbled upon a big discovery without knowing it," the researcher told them. "I have reasons to believe that those ancient symbols are actually based off a very old Pokémon. Have you two ever heard of Unown?"

"Once." James said. "My grandfather used to be a fossil hunter, and he saw them in a cave while he was digging one time."

"Well, this Pokémon apparently comes in many forms, and I believe that they are the basis for our current writing system. But unless we capture one, we won't get any more data on them."

"We should've tried to scan one down there, Jen," James said, but knew this was simply an attempt to push aside their panic. At that point, the research building door opened, and another scientist poked his head inside.

"Uh, Tom, there are a couple of strangely-dressed men out here who say they want to talk to you."

"If you need to talk to them, we can go. Thanks for getting us out of that place," Jen said to Tom, who had begun moving papers around on the desk.

"Oh, not a problem at all. Have fun exploring the rest of the Ruins, and if you make anymore inadvertent discoveries, you know where I am."

"We will!" James called back. As they left, they saw a group of men dressed exactly like the people they'd seen at the Pokémon Centre the night before. Each had the same desert camouflage trousers and black shirts, but one of them wore a grey jacket with a strange insignia on it. It looked like a bird's foot, but more angular and with three toes. The men disappeared inside, and the two youngsters moved to explore the rest of the Ruins.

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The men in the strange uniforms were all over the place, examining every structure and noting certain areas. James was beginning to get suspicious, but held back from confronting any of them. Jen also kept her silence, preferring to explore the Ruins in peace. Eventually, though, James lost patience, and wanted to find out who these people actually were.

"Who are you guys, anyway? And what're you doing here?" he asked a nearby uniformed man. "Is there something here you're looking for?"

"It's none of your business who we are, kid," the man replied in a low, grunting voice. "We're just exploring the Ruins like you, that's all. Now get lost." James' temper spiked, but Jen put a calming hand on his shoulder.

"James, it's not worth it. Let's head back to the Pokémon Centre, we've seen just about everything we can here." Just as she said this, the three men from earlier exited the research building, and the man in the grey jacket called out to the others.

"Team Triassic, we have found what we're looking for! These Ruins are the first step in our plan to rearrange the world! There is enough ancient research to allow us to initiate the next step of our master plan! We will achieve our goal!

James heard the man's words, and his temper rose.

"You're crazy! What do you think you're doing, trying to rearrange the world? And how are you going to do that, anyway?"

"Administrator, ignore this kid," the grunt James had spoken to earlier said. "He's just a troublemaker."

"No." The Administrator's voice was condescending and arrogant. "I'll enlighten him about our mission. He is a mere child, and no threat to us."

"No threat, huh?" James challenged, but Cade ignored him and went on.

"Perhaps you know something of prehistoric Pokémon?" James nodded, and the Admin smiled wickedly. "Good. They are the underpinnings of our entire operation. It is our mission to find a way to revert the world to how it was when prehistoric Pokémon still lived. These Ruins had information we needed; that is why we are here. Soon, we will change the world."

"You're not changing anything!" James shouted, and Cyndaquil squeaked at the Admin in an obvious challenge. "I'll stop you myself if I have to!"

"Is that so? But then, talk is common. Why not back up your words? You can take on my Pokémon, and then consider whether you are strong enough to stop us."

"You're on! Cyndaquil, let's show this guy we mean business!" Cyndaquil ignited the flames on his back, ready to take on anything that came his way.

"A Fire-type, how underwhelming. Now, see what a truly powerful Pokémon looks like! Kabutops, combat situation!" The Admin's Pokéball snapped open, and the flash of light gave way to a bipedal Pokémon with brown armor and a head shaped like a wider version of the horseshoe crab in the puzzle. Two sharp, curved blades extended from its arms, making it look even more fearsome. Jen gasped; this Pokémon didn't look like one to mess with. James, meanwhile, was taken by surprise.

"What is that?" He took out his Pokédex and aimed it at the dangerous-looking creature.

"Kabutops, the Shellfish Pokémon." the machine recited. "This prehistoric Pokémon has only ever been found as a fossil. It is a very fast swimmer, and its claws are extremely sharp and dangerous."

"So this thing's a fossil, huh? Makes sense, and it's probably too old and slow to beat us. Cyndaquil, let's take it down! Quick Attack!" Cyndaquil raced at Kabutops, but the attack didn't do anything significant. "Don't let up! Keep up the Quick Attack!" Cyndaquil kept hitting Kabutops, but the attacks had little effect.

"How predictable, a direct attacker. Not like I've battled any of those before. Kabutops, knock it away!" One swipe of Kabutops' bladed foreclaw sent Cyndaquil flying with little effort. Cyndaquil struggled to regain his feet, then squeaked angrily at the Shellfish Pokémon.

"Cyndaquil, don't give up! Ember!" The resultant flurry of fire bolts had about as much effect as the Quick Attack, and Kabutops just stared straight ahead, not even feeling the impacts.

"I'm assuming by your feeble attacks that you don't know Kabutops' type. Allow me to educate you, then. It is a combination Rock- and Water-type, which means your Fire-type moves are utterly worthless. Use Aqua Jet!" Kabutops dove at Cyndaquil, its body surrounded by water. The super-effective move made contact, knocking the Fire Mouse to the ground. "Now, Slash!" Cyndaquil could barely move as Kabutops' sharp blades cut him again and again, and when the Rock- and Water-type jumped away, he lay unmoving, having been dealt heavy damage by the rapid attack.

"Cyndaquil, no!" James tried to run towards his friend, but Cyndaquil struggled to his feet and squeaked defiantly, refusing to let Kabutops beat him. "That's the spirit, buddy! Don't let that old fossil beat you!"

"Predictable enthusiasm and optimism. It's almost a shame to beat you this easily. But, it must be done. Mud Shot!" Kabutops fired a blob of mud that caught Cyndaquil square in the face, sending him flying into James' arms, beaten.

"No!" Jen cried, watching as James desperately checked his starter for injuries. "Cyndaquil, hold on!"

"It's over, Jen." James' voice shook with anger; Kabutops had utterly outclassed Cyndaquil, and left him wounded. "He beat us. He's won this round."

"Yes, I have. And we are done with this place. Team Triassic, move out!" The uniformed men formed a column behind their Admin and followed him out of the Ruins. James glared after them, a tear falling down his cheek.

"Something tells me we haven't seen the last of those guys." He looked down; Cyndaquil's breathing was shallow, and he had numerous cuts on his body from Kabutops' attack. "It happened so quickly, I didn't have time to react. I should never have challenged him, or his Kabutops. Now we've made ourselves an enemy."

"Don't worry about them right now. We have to get Cyndaquil to a Pokémon Centre, and fast. Forget that Kabutops."

“She's right.” The tourist they'd been speaking to earlier had appeared. “Your Cyndaquil needs medical attention. My Kadabra can teleport you to the Union Cave Pokémon Centre; it's the only one for miles.” Jen nodded to him.

“We would appreciate that. Thank you so much.” The man let the Psychic-type out, and after he told it their destination, the group disappeared in a flash of violet light.