Four years earlier:
The legendary had been attacked by Team Rocket who had used the same machines to try and subdue him that had been used at Mt. Quena, merely more advanced. Despite the fact that he was still resisting the torture, Mewtwo had no strength left to try to escape, and so was unable to stop his captors from transporting him towards Viridian City. He knew that if he got there, they would find a way to completely subdue him, and his freedom would be completely gone.
Resisting for so long had exhausted the legendary, and he knew he was only a day or so away from Viridian. Mewtwo was resigned to his capture, and had only resisted out of his fury at having to serve Team Rocket once more. It had been clear to the Rockets who were escorting the van he had been transported in that he was being slowly broken. Mewtwo had been in the dark, too weak to even send his mind out to work out where they were, with only the noise of the van moving to focus on. That and the sound of the machines attached to the inside. As he listened, Mewtwo suddenly felt the van stop. Shouting from the driver.
An explosion. Mewtwo suddenly started paying a lot more attention, a new reserve of strength surfacing. He stayed in the van, listening hard. He heard the sounds of Pokémon attacks, lots of them. As Mewtwo waited, the number of attacks started to decline, until suddenly there was a series of massive explosions. The van rocked back and forth before settling back on its tires once again. Mewtwo waited, and suddenly the doors of the van burst open, and sunlight shone in. A figure stood at the door, only a silhouette against the light. Another silhouette appeared beside him, before a brilliantly colored beam flew into the interior of the van, shattering the four devices along the walls.
Released from the machines that had tortured him, Mewtwo dropped to the ground, landing on all fours before slowly climbing to his feet. As he looked up, the figure was gone from the entrance to the van, and so Mewtwo stepped out of his prison, into the sunlight he thought he would never see again. The back of a van was pointing up a hill, evidently twisted from the road, and in front of Mewtwo was the figure that had freed him, ten Pokémon stood in a line behind him. Slowly turning, Mewtwo surveyed the wreckage of the convoy behind him, before turning back to his rescuer.
Ash stood there facing the Pokémon in front of him. Mewtwo stood tall, but the injuries to him were. Behind him were the wrecks of more than a dozen vehicles, the bodies of many of the drivers still in the burnt out wreckage.
The Rocket convoy had been totally wiped out by Ash's Pokémon and Ash himself, Rockets lay on the ground, many of them dead. The ferocity and surprise of the attack had completely and utterly overwhelmed the Rockets, despite the large escort. Ash had personally added three to the body count, in addition to those he had only knocked out.
Mewtwo looked him in the eye, recognising the trainer that he had last seen years earlier at Mount Quena. As Ash watched, Mewtwos strength finally gave out, and he slumped to the ground.
Ash had left medicine for the Legendary to help him recover, along with a large quantity of food. Mewtwo had tried to find him to thank him, having released the clone Pokémon into the wild some time earlier .
A month later he had been flying in a remote region when he saw ruins. Dropping down, Mewtwo found that it was a Team Rocket base. In the aftermath of this discovery, Mewtwo had gone back to Viridian City. He had stood in the ruins of the Rocket headquarters, and tried to work out what had happened. An organisation that had the power to snatch a legendary couldn't just collapse, yet collapse was what had happened. What eventually clued Mewtwo in was the lack of bodies.
When he had woken up again after his rescue, there hadn't been a single body or any wrecks of vehicles left. The whole area had been cleared by Ash. Inside the Rocket headquarters was the same, so Mewtwo assumed that it was Ash who had attacked it. He never found the trainer again.
Present Day
Mewtwo stood watching the trainer to whom he owed his life. It was the early hours of the morning, the day after the failed raid. Ash was attached to the wall by manacles around his wrists. Behind him was the same machine that was built into Mewtwo's armor. It sent an electric charge into the targets body.
In Mewtwo it encouraged obedience by the simple reasoning of if he tried to resist, the charge in his armor was enough to seriously injure the legendary, potentially even kill him. It also kept him weak enough to prevent him from forcing it out quickly enough to stop it overwhelming him. The one behind Ash was enough to keep the trainer in a degree of pain, but not enough to cause permanent damage. If he tried to resist, however the charge would be turned up massively. The Rocket who had secured the manacles around him had told him so. Ash wasn't particularly inclined to test it out.
There were four Rockets stood outside the cell which was in one of the lowest levels of the Team Rocket headquarters, with Mewtwo stood outside. Tentatively, the Psychic legendary sent out his mind, wincing as the trainer on the wall jerked in pain.
"Sorry" Mewtwo's said telepathically, without the guards knowing. "If I had known it was you, I would have refused and faced the consequences."
Inside Mewtwo's head, there was an image of Ash, his body stance neutral, a shadow across his face. "It's fine. How did they catch you?"
Mewtwo sighed, it was embarrassing for him to be captured by Giovanni again. "Bad luck on my part. Giovanni was apparently looking for me, and I just managed to walk straight into a squad of his Rockets. Before I could stop them, one of them informed their boss of what they had found, and next thing I knew there was a fleet of helicopters heading for me. I was worn down over time, and a Pokémon of theirs managed to get this helmet onto my head. It has the same thing that is in your back just it was turned up far higher. In the time it took me to get rid of it, they managed to attach more, and soon I was caught, having to try to fight off the Rockets whilst enduring the pain. It was too much. When I woke up again, Giovanni was there, telling me that I would serve him, or he would kill me. Each of the pieces of my armour has one of these devices, and I can't disable them all simultaneously, their constant charge prevents me from getting back to full strength."
"If you were at full strength could you get out?" Ash asked.
"I think so" Mewtwo answered. "But that won't happen. They are sure to make sure that I can't regain strength, the power in the suits circuits is enough for that"
An image of a grin flashed in Mewtwo's mind. It was at this point that Mewtwo realised something. Despite the fact that he was closely linked to Ash's mind, he couldn't feel any pain radiating from the trainer. Yet when he watched Ash, he could see him writhing in apparent pain, something that the guards had noted. Equally, for somebody who wasn't psychic, Ash seemed to have an excellent grasp of mental communication. Now suspicious, Mewtwo started questioning the captive once again.
"Why aren't you in pain?" the Psychic legendary asked.
"I'm blocking it. Don't tell them, I can only block so much." Ash replied.
"Block? But you're not psychic, how can you block something like that?"
"Correct. Suffice it to say, I have ways."
Mewtwo stood staring at the trainer who still twisted as if he was in pain. His acting was superb, if Mewtwo didn't know, he would assume that Ash was feeling every bit of the pain that he should be. And there was something else wrong with him.
The first two times Mewtwo met Ash, he had been surprised by the amount of emotion that ran through the trainer. Now he could feel nothing. Emotion simply didn't seem to be part of his make-up anymore.
Mewtwo reached out with his mind again, surprised to feel another presence withdraw as he touched the Pokémon Master's mind. Unable to work out what the second presence was, Mewtwo decided to focus on his conversation with Ash.
"I am sorry for getting you in here." Mewtwo said, trying to apologise once again.
"I'm here." Ash said, cutting the legendary off. "You can get out."
"I can't. If I try, the suit electrocutes me."
"When I insult you, use your tail to start to strangle me."
"WHAT? Are you insane?"
Ash didn't bother to answer with his mind, merely glaring at Mewtwo and speaking out loud.
"You know Mewtwo, its funny. You were losing the tug of war when I ordered my Pokémon to pull out. A single Psychic type able to beat you. I thought you were supposed to be strong?"
Instinctively, Mewtwo growled with rage, raising a hand to strike at Ash. As he realised what he was doing, he lowered his hand, and let his tail to snake out and wrap around Ash's neck. As soon as it made contact, Mewtwo felt himself getting stronger. Energy was flowing into him, and suddenly, Mewtwo realised that there was more than enough to overload the armour and allow himself to escape.
Behind him, he heard a loud cough. Spinning around, his tail still wrapped around Ash's throat, Mewtwo saw a screen with Giovanni's face in it. The man looked pleased, as if he had just gained something important.
"Mewtwo, if you could not murder our guest, I would appreciate it."
Relaxing his tail, Mewtwo stepped away from Ash who groaned, the marks around his neck clearly visible. Mewtwo stalked away from the cell, before focusing his attention on the screen, where Giovanni was now addressing Ash.
"'Champion'. Nice of you to join us." Giovanni said.
"Giovanni." Ash replied, his voice totally devoid of emotion.
"I apologize for Mewtwo's actions. I suggest that you refrain from insulting him, he seems to take them personally."
"Perhaps he objects to his own captivity?"
Giovanni's face smiled tightly. He moved his arm, pushing a button off-screen. Ash suddenly screamed in pain, as the charge flowing into him trebled. Casting his mind into Ash's once again, Mewtwo found to his surprise that the amount of electricity that Ash was deflecting was greater than he himself was being subjected to.
To his even greater shock, he found that none was getting through to Ash. The scream was faked, making Mewtwo reflect that Ash was a stunningly good actor. As Giovanni pushed a different button, Ash flopped down in the manacles, before raising his head once again.
"I suggest more strongly that you refrain from angering me." Giovanni said his lip curling. "I don't have the same restraint when it comes to me being angered." Ash remained silent, which seemed to amuse Giovanni.
"You know you will be missed?" Giovanni taunted. "I might reveal that you fell into a trap and were captured, I might make it look like you defected. Without you able to counter the story, what Team Rocket says will be believed. And with you removed, the Pokémon League is currently leaderless, and has nothing that can stand up to Mewtwo, or our numbers. You have caused the collapse of the Pokémon League with your captivity. And to think you thought to strengthen it." Giovanni tutted. "I guess even the best intentions can end badly. I'll talk to you again soon, 'Champion'. After all, you're not going anywhere."
The screen went back. Mewtwo turned back around, before linking his mind to Ash's once again.
"'Champion'?"
"My name is a secret Mewtwo. You are among a very small group that knows it."
"You're Pokémon Master and nobody knows who you are?"
"Yes"
Mewtwo regarded the trainer, and when nothing else was forthcoming, he turned away. The Psychic type stalked up the corridor away from the cell, before walking up to topmost basement level. When he felt that there were no Rockets in the immediate vicinity, Mewtwo sent out a wave of Psychic energy from his body. Every single one of his piece of armour flew off, hitting the walls. Stretching in relief as for the first time in months Mewtwo was free from being electrocuted, Mewtwo suddenly heard an alarm going off. His face was utterly expressionless when he turned to face the squad of Rockets who raced around the corner, responding to the alarm.
The leader of the squad took one look at the armor on the floor and paled. Before he could give any commands to his squad, or even release a Pokéball, all the Rockets were lifted up from the ground and sent crashing into the wall behind them. Mewtwo then raised a hand to the ceiling above his head which promptly collapsed, giving him a route to the ground floor. Floating up, Mewtwo looked around.
The area he had come up seemed fairly empty, with not a single human in sight. Flying at the doors, Mewtwo opened them with a Psychic attack and flew out, exiting into the deserted city, before flying into the sky. Back in the cell, Ash heard the alarm, acknowledging it silently. He had at least managed to get Mewtwo out safely. The Pokémon's distrust of humans should make sure that the legendary was out-of-the-way until he had dealt with Team Rocket.
A knock on Cynthia's door caused her to groan out loud. She hadn't wanted to be at the office so early, but she hadn't had a quantities of paperwork had piled up from the various gym leaders and their trainees, and the camp had made it hard for her to keep up. Raising her voice to be audible to the person outside, she called for them to enter.
As the door swung open, Cynthia was busy scanning a report from the Cinnabar Island Gym. Without looking up, she started speaking.
"Take a seat, I'll be with you in a moment."
"I suggest you give me your full attention now Cynthia" a voice spoke inside her head.
Slowly lowering the report, Cynthia's head swung around to see a large bipedal Pokémon stood there, its arms crossed and its eyes glowing a bright blue. The report fell from Cynthia's hand as she realised just what was in her office. The Pokémon lowered its head, before reaching out to her mind once again.
"I am Mewtwo. In the absence of the Pokémon Master, 'Champion', I believe that you would be the best person for me to talk to."
Cynthia just stared. It took a lot to surprise her, but this had completely stumped her. To meet a legendary Pokémon was rare, to talk to one rarer. To have one walk into your office and start a conversation was unheard of. All Cynthia could do was a weak "ahhh"
"I didn't think this would be so hard." Mewtwo mused. "This is important, so say when you're ready."
Cynthia nodded, before shutting her eyes, rubbing them and opening them again. After deciding that there was a Pokémon in her office, talking to her, she started to calm down. Having finally gotten a grip on her thoughts, she leaned back in her chair, resting her arms on the rests, gesturing for Mewtwo to try again.
"Finally" the Legendary complained. "I need to talk to you about 'Champion'." Realising that Mewtwo knew who 'Champion' was, Cynthia was suddenly more alert. "Why?"
"Because he is being held captive inside a Team Rocket base in..."
"Goldenrod City. I know, he told me where he was going. What do you mean held captive? How was he captured?"
To Cynthia's surprise, Mewtwos head bowed, almost in shame. Her mind now working at full speed again, she was quick to spot the connection.
"You captured him didn't you? You were the trap that Team Rocket were going to set?"
"Indeed. I had been held captive with them for some time, and they had a way of ensuring that I did as ordered. A painful way of ensuring it. I was the one who restrained 'Champion' so that he could be tied up."
Before Mewtwo could say anything else, Cynthia held up a hand, before realising that Mewtwo wasn't technically talking. Despite this, the Pokémon got the message and stopped speaking into Cynthia's head as she picked up the phone on her desk, quickly dialing in a number.
"James. Hello, sorry about the hour. I need you to come into the office as soon as possible. I need some advice from you with regard to the problem." A pause. "Yes, something has come up regarding 'Champion'." Another pause. "That would be a good idea. Thank you James."
Putting the phone down once again, Cynthia turned back to Mewtwo.
"How did you escape?"
"I am unsure." Mewtwo replied. "Something 'Champion' did restored my strength to beyond the point where I could break out. I don't know how."
Cynthia looked hard at the Pokémon, before deciding that he was telling the truth. Another mystery for her to try to solve.
"Can you tell me everything? I presume you are informing me so that he can be rescued?"
"Yes."
"Right. In that case, anything you can tell me about where he is being held is crucial. When we are done here, I will start assembling trainers to join me in a second assault."
Mewtwo tilted his head slightly, regarding Cynthia before stepping away from the door. He stood facing Cynthia once again who was still sat behind her desk, before reaching out with his mind to talk once again.
"To attack the Rocket base, you are going to need a lot of trainers. Inside there are twelve floors above ground and sixteen below. The ones below contain six dormitory levels, giving the base a theoretical capacity of nearly three thousand Rockets, although there was never that many there. At most I saw several hundred, although many of these are high-ranking Rockets, so harder to defeat."
Mewtwo kept talking into Cynthia's head, describing how Ash was being held, as well as the way that he had been captured. Cynthia was typing furiously on her keyboard, writing down anything that she felt important.
As Mewtwo finished detailing the defences, as well as the location of 'Champion's' cell, the phone on Cynthia's desk rang.
"Hello? Yes, send him up. Tell the specialists to start without me today; I have things to sort out. Thank you."
Putting the phone down once again, Cynthia fixed her attention back on Mewtwo, as he confirmed that there was nothing else to say. The door behind the Pokémon swung open, and James and Meowth stepped in, jumping in surprise when they saw Mewtwo, although recognising him from events on Mount Quena. As Cynthia gestured them towards chairs in front of her desk, she sighed. Today was going to be a very, very long day.
Espeon sat at the window, looking towards the Team Rocket headquarters. It bemused her to think that she knew that the man who her trainer was trying to reach was in the building, and her trainer was captive there, yet she couldn't do anything about either. When Ash had told her the plan, she had instinctively argued against it.
The idea of leaving him for that length of time was something that jarred against her. In the last seven years, she had never gone more than a day without seeing her trainer. Now it had been five, and every time she talked to him, she was told she had to wait longer. She understood the logic, having been with him when they finally reached the crime boss's office four years earlier to find that he had escaped, but it was still hard.
She had barely moved from the window in all the time since his capture, using Psychic to bring her food to her. It was a mood mirrored among all the Pokémon that had been with Ash on the Day of Departure. The ones that had joined him since then loved their trainer, but they hadn't seen what lows he had sunk to. No words could convey the raw emotion that had been invoked in the Pokémon and their trainer that day. It was the reason that the Pokémon that had experienced it remained by their trainer always.
They refused to leave him alone simply because they wanted him to know that they would never leave him. Equally, the fury that these five Pokémon held for those that had left wasn't really mirrored among the nine.
Over the last five days these four Pokémon had waited together, missing their trainer.
Their anger towards Team Rocket for splitting them apart hadn't been sated in the first attack. When their master gave the word, they would fall on Team Rocket like a flood, to the point where they would barely need the other Pokémon.
Behind Espeon the rest of the Pokémon were killing time. In their trainers absence they couldn't train, not knowing when they might be needed. As a result, sat in the apartment that Ash had rented, they were killing time.
Many of them chose to wait in their Pokéball's, leaving Espeon, Meganium, Charizard, Sceptile, Snorlax, Sharpedo and Alakazam together waiting. When it was time to move, they would release the rest of the Pokémon before having Alakazam teleport the team to the room where Espeon could feel Ash's mind.
Without that help, they doubted that they would be able to teleport in accurately enough. Meganium came up next to Espeon, putting a vine around the neck of the Sun Pokémon. They all felt the pain that was emanating from Espeon, not least because they felt it themselves.
Meganium retracted the vine and turned back into the room, leaving Espeon to her solitude. When she reached Sharpedo, the Brutal Pokémon gestured for Meganium to follow him. After walking into a different room, Sharpedo turned to Meganium.
"What is it with you all?" Sharpedo asked. "It's like there is something special for all of you about having Ash away from us. I don't understand."
Meganium's eyes watered as she regarded her friend with a sad look. "You weren't there the day that the rest of the Pokémon left us. You can't understand."
"But what happened?" Sharpedo pressed. "What was so bad?"
"Remember Sharpedo, Ash had left all his friends. He had left his only family, all he had was his Pokémon. One of those Pokémon was Pikachu, his first and the one that he had spent every minute of his life with since he was ten. All of those left him, led away by the one he thought he could trust above all the rest. Broken does not even begin to describe how he was. Espeon and I love him. Not in the way that you all do; you love him because as a trainer he has shown you nothing but kindness. Espeon and I would die for him in an instant. Before you say that you would do the same, would you? Without thinking at all? If he was in danger, can you honestly say you would jump straight in, not thinking about anything, just focused on dragging him out alive, even if it killed you? That is what I would do for him. He has saved my life, did you know that? He has also saved Charizards and Sceptiles lives. Let alone what he did for Espeon, I don't even know her story. He had done it for many of his former Pokémon, only for them to leave him. That kind of pain cannot be put into words. On that day, I saw the human I love above all others broken by somebody he thought he could trust. On that day, those of us left made a promise. We would protect our trainer to the death, keep him as sheltered as we could. He was young, and had been through so much, it wasn't fair for anything else to happen to him. That is why we are so subdued. He is being effectively tortured, and we are forced to sit here and do nothing."