This ending does give some explanation to the attack on earth.

Ending: Sad

I mulled over the question for a few minutes. I could fight it, with May and my friends by my side. I couldn't just step down. I had come too far to run off now. Think about all the people I would let down. I couldn't live with the thought of all the friends and family that I would lose. Voices started to speak from my heart.

"You don't really think you can win, do you?" they said. "If you try to fight it, then it will kill you off." I ignored them and walked up to the creature.

"This ends now!" I summoned the blade and he understood the meaning. He pulled out his arrows and floated towards me. The others started to channel energy, but he nodded at them and they stopped. I looked down at those I know. They granted me good luck. I looked back up at the creature. It stared at me, coldly. I drifted to the side slightly as he drew back an arrow. I shot at him in a zigzag formation. He timed correctly and fired an arrow. It struck my arm and sent me spinning to the ground.

Black flames surged from my eyes and consumed the creature. It stumbled slightly, and then blue ones shot back. They lit me like bramble. I tried to stop, drop, and roll, but the flames wouldn't die down. I jumped in a nearby river. The water around me evaporated. I came out and flew for the creature. I hit it and shared the flames. We both flew around until he put it all out at once. He wrapped an arm around my throat; I couldn't break the grip. It grew tighter and tighter, until I was gasping for air.

"Humans; such fragile creatures," He said. "If you surrender now, I won't kill you or your loved one." I blew flames in his face as he dropped me. I went in for the kill with my blade. It slashed at my jacket and cut off my poke balls. He caught them and said, "If you don't surrender, I will kill all of your Pokémon, starting with Pikachu." Before I could move, he called out Pikachu, who was flying through the air. It used a Thunderbolt, but didn't get anywhere. It struck him, and he slashed with his blade. Pikachu appeared unmoved for about a second before splitting in two.

The bloody fragments fell to the ground as I started to cry. "Give up yet?" it asked coldly.

"No, because if I give up, there is no chance of survival for anyone." I darted for it, but it sidestepped and I flew over the top of the temple.

"Now you don't have a choice!" it said as a red light shot through me. I was pulled down from the sky, and onto the ring pedestal on the peak. I couldn't move anymore. I struggled to even budge an inch, but something was holding me steadfast. The same red light shot for May and started to pull her towards the pedestal. "As I promised, nor you, or your loved one will be hurt from this. As soon as May's shoes hit the ground, a red crystalline rock formed around them. The crystal crawled up our legs and to our waist before stopping.

"You are now the chosen omen for apocalypse," it said. Unable to move anywhere, I could only watch while the red crystal formed around the edge of the pedestal. It reached the rim of the ring and stopped. I looked at May while she looked at me. Tears were streaming down our faces. She closed her eyes and I did as well. I leaned in to her and wrapped my arms around her. She did the same as our lips met in harmony. It felt so warm, like a new light in the midst of the darkness consuming my heart.

Speaking of consumption, the crystal completely formed around us in a thin eggshell. The crystal around our legs retreated and thickened the walls. We then completely turned towards each other and finished the kiss. We leaned away to find ourselves in the crimson prison. We looked around, then out the shell. The originals were all healed enough to create an army of clones. They then swept over the world, destroying everything in their path. All the soldiers were roasted alive, all the Pokémon were hacked to pieces. May, her Pokémon, and I were the last things on the earth.

A loud voice boomed through the shell like a surround system. It said, "I never wanted this to happen. On my planet, humanity was a plague. They killed and hunted Pokémon. The legendary ones wanted to stop them, but were powerless and were nearly killed off by the humans. Humanity had dominated the planet, leaving very little room for Pokémon to live, forcing them into the city. There, they were often forced into corners and shot. Others retaliated and formed gangs, making life for all impossible."

"Being a Pokémon Trainer meant nothing there. There was no wilderness to explore. Whenever you caught a Pokémon from a gang, you would have to be on your guard for the rest of your life. They would hold that grudge until the day you died, by their hands or your own folly. Most trainers would go missing within a week. They would turn up the next day in a ditch or alley. Their bodies would've been chewed up with chunks missing to show the bones in some areas. The vicious gangs would've found them and just demolished them."

"I prayed to Arceus for something to happen to the humans, to set them back a step or two. When Arceus suggested that I do something, I stated that I didn't have the power to do it alone. He granted me an extra amount of power and the ability to clone myself so that I could come out victorious with an army. He supplied me with far too much power. It consumed me and sent me on a rampage. I demolished every last vestige of hope for humanity on that planet. Arceus punished me for losing control."

"He split my god like juggernaut form into 4 weaker forms. The greatest of all was isolated for what seemed like an eternity in the meteor. The others were scattered across the planet so that they wouldn't resurrect it."

"Just who are you?" May interrupted.

"If you must know, you impatient little twit, I am the entity of the true, original Deoxys. I looked nothing like the four forms that you see today."

"Then why do they continue their murderous rampage?" I asked.

"I'm getting to that part! They eventually wandered all over the barren planet until they found the strongest of all. They got on the summoning pedestals and instead of freeing their leader; they freed an immense pool of evil. It consumed their partial souls, and then spit them back up into the temple. That is where I come from. I am now the entity that posses the temple itself. My strength is much greater than theirs, but I can't do anything from this position."

"After they were possessed, they became hell bent on destroying all of humanity. They sent several hundred scouts out to scout planets. Any of them that didn't return would be retrieved. 99 of them returned, the one that went out to your planet did not. Another was sent out to search for it on your planet. It found that super advanced city, and just assumed that all of humanity was like this. If it was, then it would soon be as bad as our original planet. That is why they came to destroy you."

"Why did they save May and I," I asked.

"You two have immense power and would be perfect to draw energy from."

"You mean-" May started.

"Yes, you two will most likely never see the outside world again, but will be their private pool of energy for their next invasion." May fell into my arms, crying loudly. I knelt and cried with her. I tried to get up over time, but something was holding me to the ground. I looked and saw that the crystal was forming around me again. I was at my arms as May screamed out in terror and fled to the other side of the meteor.

"Please, help me," I cried as the crystal formed around my hands. It was ready to consume my face. "May! Promise me you'll never leave me!" I screamed. I didn't hear her reaction as my ears were already covered. A red tear fell from my eye as was nearly solidified. May came back and leaned in again. I closed my eyes and waited for about a second. Our lips met and we kissed until the crystal formed around me and spread over her face. At first she screamed, but soon closed her eyes again and enjoyed it. The crystal grew over us both and we sat there. We were frozen, kneeling, kissing for about ten years.