Kanto – Cerulean Cave – Nighttime
"I was mistaken." Mewtwo admitted. "I thought Entei had survived because a very strong Fire Pokemon suddenly emerged in Ilex Forest. The Pokemon was close to the Ruins of Alph and was way too powerful to be a wild Pokemon. But it was nothing more than a Typhlosion, perhaps summoned by a trainer. Or perhaps a Quilava evolved. All I know is that it was not Entei."
"…" Suicune cried quietly.
"I apologize for giving you false hope. I was…perhaps using any minor occurrence to convince myself no one was able to kill a Legendary Pokemon. It would also suggest that Raikou and Ho-oh had survived as well. That they had all simply fainted like in any battle. This false hope…I have done us both a great wrong."
"I forgive you…but what is to come of us now?" She asked.
"…Where is the egg? The egg which you and Entei created?"
"I have tied it in my hair, so I don't have to bite on it to carry it." Beneath the long, flowing folds of hair, the egg was barely visible.
Mewtwo began to give her instructions. "Good. Take your unhatched child and seek shelter with Regice, in the land of Hoenn to the south. It, Registeel, and Regirock are the most secretive, isolated, and protected Pokemon in the world. You and your child will be safe there."
"Is it really?"
His frown was barely visible in the moonlight. "In times to come, no one is truly secure in any fortress. But you're safer there than here, anyway. With your escape, Lugia is the only Legendary left in Johto. I fear nothing he can do will grant him survival. He can only decrease their numbers and attempt to drive them away from the rest of us." He turned his back. "Now, let's go."
"Us? Why are you coming?"
"I need to form an alliance with a mortal enemy."
Johto – Whirl Islands – Open Seas
Lugia soared south through the night sky. The Unown were in hot pursuit! But he sensed they were using all their energy to keep up with him; they normally moved very slowly. Even better, his distraction to lead them far away from the other Legendaries was working; they weren't far from Cianwood City.
"You'll never catch me. Barrier!" Lugia created a giant Psychic wall that stopped them! They managed to break it, but at a good cost of effort. As the chase continued, he constantly slowed them down and reduced their energy.
When they were just outside Cianwood, Lugia turned around and used Psychic! Though hundreds in numbers, about a dozen fell dead into the sea! They simply had used too much energy. The many remaining shot a ton of Psybeams! Lugia dodged and spun into the sea! The assault stopped. The Unown Cluster flowed in midair, confused.
"Spiral Tempest!!" Lugia swirled out of the ocean, creating a massive tornado of water! Trapped inside, the Unown shot hundreds of small orbs that caught onto him and zapped his body!
As Lugia began to die in the chaos of both attacks, he raised his head and began charge an incredible energy in his mouth. "I will drag you all down to hell with me! Mega Aeroblast!!!" A huge beam of light, thick as a small town, blew up into the Unown! His energy completely used up, Lugia fell into the sea…
Kanto – North of Vermillion
Mewtwo and Suicune were running hard to Hoenn. But Suicune wondered how they would manage to get there. "But Hoenn is far across the sea south of Fuschia! How in the world will we manage to get there?"
"We're going to try and stowaway on a cruise ship in Vermillion. They almost always stop by the Sevii Islands, the midpoint between Kanto and Hoenn. But we don't have much time; it is late in the night and the last ship is bound to leave soon. Hoenn isn't-"
Suddenly, a huge roaring occurred and the earth shook! In the distance there was a pillar of white energy. Mewtwo frowned. "It's Lugia's Mega Aeroblast."
Suicune shuddered. "You mean…?"
"We have less time than I thought."
Johto – Ilex Forest
Entei/Typhlosion looked around the night in panic. "How did I get this way?! This is impossible! I can't believe this…I'm stuck!" He took another look at himself and sighed. "I guess I just have to get used to being a Typhlosion. At least I got a canine Pokemon, which is similar to my real body. I mean, I'd be really confused as a Tentacruel or Electrode. In any case, it's better than death."
From the nightlit forest's bushes an Ampharos appeared! Entei swirled around, but fell! Typhlosion were able to walk like bears; either on two legs or four. He had tried two legs, which he wasn't even remotely used to. Entei quickly got back on his feet. "All right, who are you and what do you want from me?! There are never any wild Ampharos around here."
"I could say the same about a Typhlosion!" Was the reply.
They both processed this information.
"…It can't be….Raikou?"
"…Entei?"
There was a pause. "Oh my god!! You're alive!!" They yelled and hugged each other.
Entei walked back and saw Raikou's new form. "Dude, look at you! You're an Ampharos!"
"And you're a Typhlosion!"
"…How in the world did we get this way?"
"I don't know, Entei. But I-"
Suddenly, the forest was blasted through! The Unown Cluster floated towards them! They were as large as ever; a sphere as tall and wide as Tin Tower.
"We can't fight like this! Hide!" Entei yelled, ducking behind a tree. But the Unown simply ignored them and continued floating east.
Once the chaos was over, they emerged from behind the trees. Entei cursed. "Damn it! They're still alive! My sacrifice meant nothing!"
"Mine too! Can anything stop them?!" Raikou demanded.
"Apparently, something isn't us." Entei scratched his head. Then he noticed something. "They didn't attack us."
"Yeah, that's freaking weird. Why not?"
"I mean, these things are hunting Legendaries and they completely ignored two of them right here!"
"Hmm…" Then Raikou understood. "They ignored us…because we're NOT Legendary."
Then Entei got it too. "We're just an Ampharos and Typhlosion…Maybe this does have some advantages…" He remembered something. "Oh, god! What happened to Suicune?!"
"Relax; I told her to run to Mewtwo and tell him what happened. She did. Both her and the egg are safe."
He sighed in relief. "Thank goodness. But I just hope you're right. Because the Unown are headed for Moltres right now. And if they finish him…"
Kanto – Victory Road
In the darkness of the cave Moltres could barely see the Unown approach. He quickly opened his eyes and shot a Flamethrower! It too was blocked by the shield. The Unown cast Psywave! The cave shook and exploded! Moltres was blown up to the top of the mountain near Indigo Plateau.
"Pyro Swirl!" Similar to Lugia's Spiral Tempest, he created a tornado of fire! "Fire Beam!" Moltres shot a thin beam of concentrated energy at the shield! The Unown quickly dissolved the flames!
"Psy Doom." The Cluster cast a special Psywave Confused, Moltres didn't immediate notice the attack's effect. But then his muscles began to bulge! The veins in every part of his body, especially the head, were pulsing and clearly visible.
"Wha…whaaat havvve yoooou dooonnne toooo meeee?!?!" Moltres gurgled. Then, one by one, his brain cells began to die. He flew up in a drunken-like manner and began to make random movements, bashing his head into rocks and boulders. Poor Moltres began to laugh like a maniac as his brain fried.
Then, in one instant of this ranting, his brain exploded. Blood leaking from the ears, eyes, and mouth, Moltres fell down to the earth, dead.
Kanto – Vermillion City – Docks
Suicune and Mewtwo jumped on top of the cruise ship's roof! Fortunately, it was so dark at night that none of them humans could see them.
Mewtwo turned around, sensing Moltres's horrifying demise. "N-n-no! They're already that far?! Damn it, Moltres! Why didn't you run?!"
"Why aren't the other Legendaries listening to your warning?" Suicune asked.
Mewtwo gritted his teeth. "Grr…Lugia paid attention. He knew he was doomed anyway, so he sacrificed himself to try and lead them away from us. But Ho-oh and Moltres…they're too damn caught up in their pride! They won't listen to me because I'm the youngest of us all. It's these cursed old rivalries! The thought of all Legendaries getting even close to tolerating each other is unfathomable. The history of Legendary relations is tainted with power struggles and border disputes. Lugia and Ho-oh. Groudon and Kyogre. The 3 Dogs of Johto and the 3 Birds of Kanto. Celebi, Jirachi, and Mew. Regice, Registeel, and Regirock all versus the Unown. And…"
"And what?" She was curious as to whom Mewtwo was rivaled with.
"Rayquaza, Deoxys, and myself. Rayquaza, born of the earth. Deoxys, from outer space. And me, created by humans through science. We all represent our origins, which naturally oppose each other."
He continued. "They especially hate me. I represent humans. I was created, cloned, just for them to prove they can and feed their pride. If there are two things Pokemon hate about humans, it's their selfishness and pride." Mewtwo looked down sadly. "In times like those spent fighting Rayquaza and Deoxys, it feels like I have to answer for the actions of mankind."
"…" Suicune processed this information. "…That's not true. Is Rayquaza the cause of every earthquake? When creatures from space invade earth, do we blame Deoxys? No! Is it your fault that humans drove Mew, your predecessor, to extinction? Of course not! You're not any more responsible for humanity than Deoxys is for space and Rayquaza for earth."
Mewtwo thought about it and smiled. "You are right. What on earth was I thinking?"
"Well, don't ask Rayquaza what it was." She laughed.
Johto – Ilex Forest
"So...what do we do now? How do we return to our original bodies?" Raikou/Ampharos asked.
"We don't know yet." Entei/Typhlosion admitted. "But I think the Unown attacks are more-"
"Shh. I hear something." They waited, silently. The noise was gone, for the moment.
"It's gone." Raikou sighed.
"Well, that-" Entei began.
Suddenly a Fearow swooped down and attacked! Entei and Raikou barely dodged it! "Hey! You wanna mess with us?!" Raikou taunted.
"This is my territory! A wild Ampharos and Typhlosion in Ilex Forest? You're up to something and I'll find out what!" The Fearow landed and began to charge up an attack in his mouth. "Flamethrower!"
"What the hell?!" Typhlosion just barely dodged it. He was expecting a Hyper Beam at most. "That's impossible!"
"A Fearow did what?!" Ampharos yelled.
"Fearow?! What are you talking about?!" The fire-breathing bird demanded.
Typhlosion/Entei thought about this. "…Oh my god…Ho-oh?!"
"Of course I'm Ho-oh! What do you think I look like, a Fearow?!"
Ampharos and Typhlosion nodded. Fearow/Ho-oh looked into a nearby pond. "Aack! What the-?! How did this happen?!"
"Ho-oh. It's me, Entei. And the Ampharos is Raikou. When the Unown killed us, we were reborn like this. I don't know why, but-"
"Entei?! Raikou?! What is this sorcery?!" Then Fearow grinned maliciously. You haven't seen a wicked smile until you've seen a Fearow do it. "Fortunately, now that you're weaker, I can finish you." He began to charge up another Flamethrower! But he was hit by an Ice Beam from behind! Fearow was frozen up to his neck!
"Don't forget you've gotten even weaker than they are, Ho-oh." A Milotic taunted.
"How dare you…release me at once!"
Typhlosion's eyes widened. "…Lugia?"
"Yeah! I can't believe it either!" Milotic replied. "It's gonna be an adjustment, though…"
"…I'll have my revenge!" Ho-oh/Fearow burned through the ice and flew away!
"Wait! Come back!" Ampharos yelled.
"Let him go." Entei said. "We don't need the likes of that old buzzard. So, Lugia. You're…a Milotic."
"Meh. No Psychic and flying Pokemon ever loved the sea more than I did. Though it'd be nice to be reborn as a Xatu. So, wow. We're all alive and in the flesh! Er…some kind of flesh. I'll be off now."
Typhlosion stopped him. "Lugia. You know how much I hate to ask this…but we may need to put our differences aside for now. I know you've never really gotten along well with Raikou and I…but this is bigger than any rivalry any Legendary has. The Unown need to be stopped. And we all need our bodies back. You hate the Unown, we hate them. You need your old body, we need ours. And I'm pretty sure there's only one way to do these things at all. So we might as well work together for the same goals. So what do you say? A truce until the Unown are dead and we're all back to normal?" Entei reached out his paw, ready to shake hands. Well, with a paw and tail fin or…whatever.
"…" Lugia went into deep thought. "…All right. I suppose it won't be so bad. Truce." He wrapped his Milotic tail around the hand and shook.
"So, you've clearly seen more events than we have. What was going on when you died?" Ampharos asked.
Lugia/Milotic explained. About Mewtwo's broadcast. How Ho-oh foolishly charged at the Unown and was sent to his death. How Lugia had driven the Unown as far as Cianwood City, southwest of the Whirl Islands.
"So…Suicune made it to Mewtwo and delivered the message. That's good." Ampharos sighed.
Typhlosion smiled. "I'm just glad she's safe. But she's the last Johto Legendary. They'll be after her now."
"I think she'll be okay." Milotic said. "Moments before I died, I sensed that Suicune and Mewtwo were headed south and near Saffron City."
"They were between Vermillion and Saffron, heading south?" Ampharos processed this information.
"Oh! They're getting on a Vermillion ship!" Typhlosion realized. "They're going to the Sevii Islands near Hoenn!"
"…" Ampharos remembered something. "There are only two reasons he'd go there: Going further to Hoenn, or to seek Deoxys."
"An alliance…between Mewtwo and Deoxys?" Typhlosion couldn't believe it.
Milotic frowned. "If Mewtwo's that desperate, then the situation's worse than we thought. He'd rather die than beg Deoxys for help."
"Which means he thinks losing to the Unown is a fate worse than death itself." Typhlosion said.
"…Wouldn't that be our fate?" Ampharos pointed out.