Present day…

Mismagius woke up for the ninth time. She looked around and was still in the same predicament. Apart from her dizziness over the battle, her hat was missing, and she had a collar around her neck that prevented her from going intangible. She was locked in a room by herself.

'Confusion,' She thought. 'I can't think straight.'

She waited until her vision focused, and finally spotted her hat on a table across from where she was, but could not glide over to it because of the collar. She needed something to pry it off.

"Or someone…" She spotted a Growlithe, asleep by the door. "Hey, you," He woke up with the sound of her voice, and stared at her blankly before scoffing.

"Keep quiet," He said.

"Oh…that's a lot of talk coming from you," She said. "Where's your trainer?"

"I don't need one, unlike you," He said.

"Oh?"

"You're nothing without your trainer, and he's nothing without you," He said. "I wouldn't wait one second before scratching his eyes out with my claws."

That gave her an idea. "Really now?"

"Yes," He said, with an evil smile appearing on his face. "Your trainer is weak. That's the reason he hasn't saved you. And the moment I see him…I'll make sure he knows why."

"Touching," Mismagius said. "And they say your kind is loyal…you're just a mutt like all the others."

He got up. "What did you say?"

"You heard me, you're a mutt" Mismagius chuckled. "Only a fool can expect you to act so low…Morgan, is it?"

"Don't you dare disrespect Dr. Morgan!" He growled.

"What do you plan to do about it?" She asked. "Defend him? Why doesn't he come down here and defend himself…oh that's right, because he left a mutt to do a man's job."

He howled, finally gathering enough anger to try and kill her. He bit her by the neck and threw her against the wall, before lunging at her, claws extending. Mismagius raised her head to avoid eye contact and he pried his way through her collar, destroying the device. Before he could land a finishing blow, she stopped him.

"My move," She propelled him towards the wall, and he collided hard, eventually sliding to the ground and attempting to get up again. She in turn, used hypnosis, and put him to sleep, and then drained what energy he had left through his dreams. She took a deep breath, and put her hat back on. "Much better."

"What the hell is going on in here?" The door burst open, and two guards came in, attempting to call for backup now that Mismagius was free. She took their radios, and dismantled them before their eyes. "WE HAVE A PRO—" She stopped them before they could finish, putting them to sleep and throwing them back into the room and locking the door.

"Problem?" She finished. "Can't spot it."

Latias had been moved to a new cell, and she and Rayquaza had been separated again. Five days had passed since she last saw him, but she could hear his roars and shrieks coming from a place she couldn't pinpoint. She curled herself up in a corner and started to whimper, covering her face with her paws.

'I'm next, I know it,' She thought. 'I can't imagine what they're doing to him, but—' She heard another roar, and cringed, now starting to cry. 'Calvin, where are you?'

Lights flickered on. Latias looked up, and she was now in a grand cavern. She turned to look at Morgan, who was standing on a balcony high above her, with some scientists. She started growling.

"Getting mad at me won't help your case," He said, voice echoing through a microphone and throughout the cavern. "You have bigger things to worry about."

A door opened on the other side of the cavern, and some men wheeled out a huge steel box. It started to rattle violently, and eventually what was inside it started prying its way out and when Latias finally saw what was inside, she gasped in horror.

It was Rayquaza…at least that's what she thought. His skin color had changed from emerald green to lifeless gray, and all his markings, which glew yellow at some point, were now glowing blood red. His pupils, unlike all of his discolorations, were blue in compliant with Morgan's eyes. When he spotted Latias, he roared in fury.

"Rayquaza!" She yelled. "What…what have they done to you?"

"Since I couldn't find anyone with the guts to test out his new strength," Morgan continued. "I reminded myself. Why not Latias?"

'You're sick!' She yelled back. 'I would never try to attack him!'

"Good luck, then," He waved his hand. Before Latias could react, Rayquaza whiplashed her with the edge of his tail. Latias flew back, but caught her ground.

"Rayquaza, listen to me!" She cried. "I refuse to attack you! I'm your friend!"

He roared and continued battling.

I stared at the ceiling all night while lying on my cot. With Molly's fate unknown and Latias's whereabouts up in the air, I was clueless about how I was going to escape this place. Would it have made a difference, is what kept bugging me. I couldn't just leave them behind. Suddenly there was a roar. I sprang up out of my cot and walked to the door. I couldn't see anything from this angle of the hallway. I sighed and paced. I couldn't think of anything that could calm me down until I remembered that mom was visiting. That only made it worse.

I checked my watch. It was Wednesday, and Christmas day was tomorrow. What would she say when I wasn't there to greet her? That Molly wasn't there to greet her? I sat down on the edge of the cot, wondering about these two things, when voices, probably guards standing outside my door, started to panic. There were sounds of a fight.

"What the hell?" I walked to the door again. I could see two bodies lying motionless on the ground before a set of eyes interrupted my field of vision. I jumped back. "Whoa! Mismagius?" I wanted to hug her, but like always, I passed through her, colliding with the hard metal of the door. Nice going, Calvin. "How did you…where have you been?" I asked rubbing my head. "You know what…never mind that, help me get out of here,"

She nodded, and her eyes glew, eventually opening the door. I walked out into the hallway. "We have to get the sword back," She nodded again, and we ran down the hallway, eventually spotting another door. I looked through the slot. There was a lab set up in this room, and two scientists had the sword under what appeared to be a huge scanner, and up on the computer screen, I could see fragments of information popping up. I couldn't let them know about it; it was an easy ticket to finding Arceus…again.

"Mismagius, I need you to—" She was already in the room. When the scientists finally noticed her presence, they tried calling for help, but she threw them to opposite sides of the room, and they fell to the ground, unconscious. The door clicked open, and I quickly picked the sword up from off of the scanner. "What was that all about?"

"I'm very frustrated at the moment," She said. "The quicker we leave from this place, the better."

I heard another roar. It didn't sound like Latias; it was more aggressive, much louder, and every time I heard it now, the floor rumbled, or there was a loud blast. "Could it be…Rayquaza?"

"It makes sense," She said. "Let's find out."

We ran back into the hallway, and just a short distance down, we were approached by that same Dragonair that attacked us back in Alto Mare. I unsheathed the sword and prepared to attack. She stood her ground.

"You're not going to win this one," I said to her. "Get out of the way."

She reached for something, and I was about to attack, but a closer look revealed that pokéball that that guy used to capture Latias in. She threw it at me, and I caught it.

"That's the one my master used to capture the Rayquaza with," She said.

I looked at it, and then crushed it beneath my foot. Then looked back at her. "Why are you doing this?"

"I've opened my eyes," She said. "I've seen the things Dr. Morgan does, and it's about time I chose a side."

It would explain a few things. She didn't strangle me to death back when we were ambushed…and Molly… "What happened to Molly?"

"I don't know," I didn't believe that.

"You were there! How can't you know?"

"I didn't want for this to happen," She said, crying now. "I hit her with a jet of water, just enough to get her to the ground…but that Infernape…be broke her ribs…and we just left her there, to die in the rain…"

Broken ribs…there was no way she could continue battling after a vicious attack like that, but that doesn't mean she would just lay there to die. "Let me tell you something," I raised the sword to her. "If you're lying and something much worse happened to my daughter…you better hope I never see you again."

There was another explosion. She shivered.

"You'd better hurry. That Latias will not be able to continue holding off that Rayquaza."

"What?"

Latias engulfed herself in an orb. This would hopefully protect her from Rayquaza's attacks, but she was becoming increasingly fatigued trying to, and she had been injured in the process. Rayquaza, in turn, bit down on her orb in an attempt to break her concentration, but she was putting up a very good fight. He threw her against the wall, orb still in place, and hit it with his tail. Latias was trying her hardest to keep the orb up.

"Rayquaza, please, Stop!" She yelled. "You don't want to do this!"

Her pleas weren't getting through to him, because when she looked up, an orb of light had appeared in his mouth. It grew larger and larger, until she recognized the attack as hyper beam. She put as much energy into the orb as she could as he fired his attack, exploding on contact and covering the area in smoke. The intense battle had caused parts of the cavern roof to buckle.

"Sir, we have to leave," A scientist said to Morgan. "The constant and sudden vibrations of this battle are destabilizing the mountain's infrastructure. We will be under piles of rock in a few minutes."

"It's time to leave then, gentlemen," He said. "Pack up. We're heading back to Sinnoh. Our work is done."

The dust cleared. Latias's orb had failed; she was lying on the ground, beaten and barely conscious. Rayquaza was recovering after his hyper beam, but was ready for another order. Morgan smirked.

"I hate to leave on such short notice, Latias," Morgan called. "But farewell for now. Rayquaza, finish her off."

Rayquaza, now recovered, prepared for another hyper beam. Latias, tears flowing through her eyes, was too beaten to dodge, and only looked up into an inevitable fate. She then covered her eyes as he fired his attack. Everything slowed down. She looked again, and to her shock, she saw what appeared to be a dark figure, in the shape of an eon dragon.

'L-Latios?'

'It's not your time yet, Latias.'

There was an explosion, but nothing happened to her. When she looked up, the figure had disappeared with the light, and was replaced by a human.

"Calvin? Is…is that you…?"

"Yes," He said weakly, having blocked the hyper beam with the Archaic Sword. "Are you alright?"

"I…" Having seen enough, she lost consciousness.

Latias fell unconscious. I ran to her side, but she was out cold. I gritted my teeth.

"Morgan…" He tried to walk off the balcony he was standing on, and as I tried to run after him, Rayquaza whiplashed me with the edge of his tail, sending me flying across the room. I barely caught my ground and dealt with the pain, and gazed at the discolored dragon. There was nothing but blood in his cold blue eyes. He lunged towards me.

"Mismagius, psybeam!"

She fired her attack at him, hitting him directly in the eyes and causing him to hit the wall above us. He cried out, trying to restore his vision. I spotted some cables in a corner of the room. Hopefully they were electrical, and the shock would paralyze him. "Again, Mismagius!"

He fired at his chest, pushing him back more.

"Again!"

She fired again, pushing him back until he was directly over the cables. I ran up his snake-like body, until I got on top of his head, and then fell back. My weight was just enough to knock him off balance and he fell to the ground; one of his horns puncturing the cables, sending an electric current up and through his body. I jumped off before I could be affected. Slowly, his colors started to revert to normal, and he fell unconscious, and everything went quiet. I looked back to the balcony. Morgan had disappeared.

"Damn it!" He got away…again. Fortunately he wouldn't get away with any of the information he had recovered from the sword, so Arceus was safe for the moment. Rayquaza roared again and I armed myself, but this time it was a roar in pain. I took a deep breath.

"Calvin!" He looked at me. "Are you alright?"

"Are you serious?" I looked at him. "You just tried to kill me and Latias and you're asking me if I'm alright?"

"Latias!" He immediately got up and flew over to her body. "Latias…is she—"

"She's alive," I said. "But you…what the hell is wrong with you?"

"It wasn't me, I swear!" He said. "I tried to stop myself from doing it, but I couldn't…" He held his head. "These voices were in my head…it was like they were controlling my every move…"

"What makes you think I'll believe that?" I asked him.

"I would never hurt Latias, never," He picked her up. "She's the only friend I've got…"

It must've taken some courage to say that out loud, because he meant every word. And as I started to think it over, he had no control over his body and he attacked the ones he knew was closest to him. I looked at Mismagius.

"This song has already been sung, Calvin."

"Not mind control again," The skin discoloration I witnessed must've been some kind of side effect.

The ground started to rumble again, and it was soon followed up with falling rocks. Rayquaza shielded us with his body. "This place is coming down! We have to get out of here!"

"Rayquaza, were you conscious when they brought you here?" He nodded, and we climbed onto his back while he carefully hoisted Latias up to safety. "Lead the way!"

He took off, back down the hallway, as the ceiling above us finally gave way. He darted around the tight corners until we came to an opening. It was so good to see light again. We exited the tunnel, with the entrance collapsing behind us and sealing the mountain off again.

"Do you think he got away?" Rayquaza asked.

"I don't care," I said. "We need to get Latias home, and fast."

It was a decision I had a hard time making. Molly was out there, somewhere, and unless she miraculously found a way to get some help for her injuries, the rain would've dealt its toll. I turned my view to the sky, not looking back, and Rayquaza took off in the direction of Alto Mare.