Back at the damage area, the authorities are sent to investigate. Officer Jenny leads a navy squadron to the recovering area. Looker and Cynthia eventually make their way to the site and take over the investigation. They board a small navy boat where Jenny greets them.

"Officer Jenny, give us something useful," Looker commands.

"So far, there have only been traces of debris and metal remains," Officer Jenny relays the findings. "We suspected it to be a base. Or a secret compound."

"Any bodies recovered?"

"Negative, sir. Not a single Pokémon."

As they sail towards the site of the annihilated Team Rocket base, Cynthia's instincts kick in, ready for any assault.

"Zero traces of humans. Or Pokémon. What do you think?"

Cynthia has her eyes on the ocean. A clutter of debris is still floating on the sea. So, it is impossible to detect any human traces. Thus, she insists, "We have to dive below."

At her command, the law enforcement suits up in their scuba gear and brings out a squadron of Prinplups to head for an underwater search. Cynthia and Looker suit up as well, with the former given a Wartortle for the investigation.

As they dive to the site, dark smoke spews and mixes with the water. Looker navigates to one barge that is right in front of them. Cynthia steers her Wartortle below the barge.

"Looker, we need to light the way."

Looker then signals for several officers to light up the way using waterproof searchlights and mini-submersibles. Once the way has been cleared, they discover the submerged remains of the Team Rocket warehouse. Cynthia even notices an insignia.

"Team Rocket, how were they able to set up a headquarters here?"

"One way to find out." Looker then leads Jenny and the rest of the officers to the ruins below.

The warehouse ruins are those earlier that contained the experimentation room that held Caliban and his master Tamerlane. Thus, the search team traces the sunken remains of the devices used.

"Team Rocket must have been experimenting with Pokémon; that is certain," Officer Jenny deduces.

"Not just that," Cynthia says. She then shows them nearly cracked but glass plates, where the Team Rocket scientists wrote down their plans and mapped out the area. "They have been scanning the area."

"For what?" Looker asks.

The Sinnoh Champion notices a white mark from the glass. "This. Ratman site."

"Ratman, what is that?" Looker asks.

"Not sure." Cynthia then orders the team, "Quick, let's piece them together!"

In response, the law enforcement team searches around the submerged warehouse for the other parts of the glass. It is a strenuous task as some parts scatter around the site and several are dropped to the ocean floor. But with swift determination, the team succeeds in retrieving them and piecing them together. The end result is something that Looker and Cynthia could not believe in.

"What is it?" Officer Jenny queries them.

"It is the entire region," Cynthia ominously replies.

The glass formed was the entire Pokémon area that stretches from Kanto to Kalos to other neighboring regions. And in the middle parts of the map and the surrounding regions are labelled "Ratman site". But in the middlemost part of the map is labelled as "Ratma", with red arrows pointing at other regions.

Meanwhile, back at Professor Rowan's laboratory, the renowned Sinnoh professor calms down Barry from the distraught that he faced earlier.

"Are you fine, lad?" Rowan asks him.

"Yeah…I guess so," Barry replies.

The professor sits beside him and pats him in the back. "Barry, it comes to this point that we would really need your help. And I need you to tell me everything that happened."

"I'm not sure," he hesitates, "I mean I made a mistake."

"Look, Barry, we all made mistakes. And sometimes, we can't forget about them. But you can set it aside for a while. Just tell us what happened."

At the edge of his breath, Barry finally resolves to sharing everything he knows from the destruction.

While that is going on, a 4x4 jeep hurtles towards the professor's laboratory in full speed. The driver is wearing a full explorer gear over his black attire. The radio on his car broadcasts the latest report about the Sinnoh blast (with the whereabouts and the people responsible being yet to verify). But when the reports mentions about Team Rocket, the driver quickly turns off the radio.

He parks immediately in front of the lab and gets down from the vehicle, revealing him to be up-and-coming Pokémon researcher Gary Oak. Since he is an apprentice of Professor Rowan, he instantly postponed his field work and headed to his lab to assist in the investigation.

Rowan's assistant briefs him, "Gary, great you could be here in the most opportune time. We had already sent a search team in the site. But we discovered that the site was covered by…"

Gary interrupts him and asks, "Where's the Team Rocket grunt you caught?"

Professor Rowan suddenly notices him. "Gary, my boy, you came."

The junior Pokémon Researcher then goes to him and shakes his hand in response. "Always my pleasure, professor. So what do we have?"

"Well, Barry here found her. He escaped from the site after being imprisoned."

"Oh, a brave trainer."

"It's all me," Barry brags. He then introduces himself to Gary, "Barry, son of Palmer, the Frontier Brain in Sinnoh."

"Oh, I heard a lot of good things from him."

"Yeah, such a cool dad." But his tone is not that confident.

"Alright, what's your story?"

Barry then exposits his entire story. "Look, I didn't mean to cause trouble. I just dove into the cove in just hopes I can see a hidden item. Then, I saw this giant fossil. I thought it was a Pokémon. So, I tried to pull it out, as well as this other rock thing that looks like a human. But Team Rocket showed up and snatched the fossils from me. And they locked me up. But weird thing is those fossils that were supposed to be mine came to life. They were really, really powerful. And they go boom. And they went bang! They were all over the place!"

But Gary calms him down from there. "Okay, take it easy. Just tell me what they are. Where do they come from?"

"I overheard from their leader, Giovanni, they were ancient Pokémon. They were trying to extract their power. But the two overpower them."

After getting the information that he needs, Gary confronts this to an ailing Matori, who is kept at watch inside an empty room. Her hands are cuffed to the table, leaving her with a glass of water and painkillers at her right. Gary sits right in front of her to address about the secret base. "Matori, it has been a while that Team Rocket would be prominent in such a catastrophe. I thought they would quit like some of the criminal groups in some regions. But now, you are here."

"Cut to the chase, and what do you want?" Matori harshly intervenes.

"Well, I thought you might not ask. Where is your boss?"

"Does it matter where's my boss now?"

"Just answer the question, Ms. Matori. We want to make this perfectly adequate in your part. Tell us your activity, and maybe we could set you free."

"Why would I buy into your game if in the end, you will just consider me a criminal?"

"You're not helping yourself, are you? You've been helping Giovanni for a long time, and you still have no idea where he is." Gary then shifts from becoming intrusive to being concerned. "Look, Ms. Matori, if you wish not to cooperate, tell us what do we need to know."

After hearing his request, Matori can only utter an ominous chuckle. "You know too much, grandson of Samuel Oak. It was so dedicated of you to honor your grandfather by investing on his place. Well, for that case, let me tell you something: I might not last long, neither are you or anyone else in this laboratory." From the other side of the room, everyone else overhears that claim. "The end has been unleashed. On that very point, the end shall appear right before them."

Professor Rowan quickly realizes that Matori is referring to the diving team sent to investigate on the side. He alerts them, "Rowan to Cynthia, over! Abort mission now! Abort!"

Back to the team, they document all of their findings with the use of cameras and detectors to place them in a digital file. However, a school of Remoraid suddenly sweeps right in front of them, distracting the team.

"What was that?" Jenny asks.

"Remoraids," Looker confirms. "But they are swimming to one direction."

Cynthia then reels out of the warehouse with the Wartortle to see if other Water Pokémon reacted the same way. Sure enough, they do, as more schools of Fish Pokémon flee away from the sunken base. "Looker, Jenny, we better move to the surface."

But suddenly, she overhears the sounds of screaming and panic from the sunken site. Right away, Cynthia goes back. "Wartortle, dive back in!"

When she returns, Cynthia witnesses an army of eel-like Pokémon puncturing to the chest of some team members. The Prinplups unleash Water Beams towards the eels, which become partially effective. However, they fight back and sting them until they are down.

That leaves her, Looker and Officer Jenny below.

As Sinnoh Champion, Cynthia insists to fight the demeaning Pokémon on her own. "Looker, Jenny, you better come back to the surface at once! I'll fight them off!"

"But Cynthia…" Looker replies.

"GO!"

At her insistence, Looker and Office Jenny quickly go back to the boat and head away from the site to alert the rest.

Meanwhile, Cynthia orders Wartortle to divert the eel Pokémon and lead them to a nearby cove. When they do, the Sinnoh Champion returns Wartortle and waits for the eels to strike.

The mysterious Pokémon at their most menacing hurtle their way to strike Cynthia, but the latter calls out Garchomp from its ball. "Garchomp, Poison Jab!"

And there goes Garchomp, beating the breaching eel Pokémon, one by one. It is not easy as some eels sting to its claws.

"Don't quick, Garchomp! We have world to save!"

Motivated, Garchomp leaps from the rocks and beats down the continuous schools of eels.

For the final blow, Cynthia commands, "And now, use Dragon Claw!"

At her command, her signature Pokémon unleashes a delicate move that knocks out the rest of the eels and sends them back to the ocean.

The partners take a rest from that swift encounter. "Where did those Pokémon come from? Come on, we better investigate."

But before the two could get off the cover, Tamerlane and Caliban teleport to the other end of the cove. The dark master is rather impressed at Cynthia's prowess.

"That is fascinating. You are one of the most instinctive trainers that beat my Pokémon," he says in a smooth way.

"You are the one responsible for the attack!" she deduces.

"How could you say? Just because I was able to conjure an army from a kind that your kind shunned away from."

"What are you talking about? Who are you?"

"Glad you may ask." He then slowly approaches her.

There is no escape for Cynthia, as behind her is already the ocean. Thus, she sends out Garchomp for another attack. "Garchomp, Dragon Claw!"

But as Garchomp is about to charge, Caliban unleashes an energy ball towards the Pokémon that immediately knocks down the Dragon type.

"Return!" Cynthia commands. But before she can make a move, Tamerlane conjures a Z-move out of his very hands and combining with Caliban's power, controls Cynthia telekinetically so that they may bring her closer to them.

Cynthia tries to escape, to no avail. "LET. ME. GO."

"You are a unique girl," Tamerlane ominously utters. At the touch of his hand to her hand, the ruthless master receives information about the Pokémon world and everything that surrounds it. It is more of transmitting Cynthia's knowledge to Tamerlane without draining her knowledge.

But in the end, Cynthia ends up drained and traumatized. She also connected mentally to Tamerlane. "Who…are…you?"

But Tamerlane never responds, as he is self-absorbed on the knowledge he has. "Finally, the world is at my grasp." He then looks towards Cynthia. "And you get the dubious honor to witness how this world shall recognize what they have done to the Ratman region!"

At one snap, Tamerlane, Caliban and Cynthia vanish from thin air.