It has been three weeks since Ashlee's best friend Eyan transformed into a Latios and left Clearwater Town, with not one person knowing where he is today. She has spent much of that time at the cliffside looking out into the horizon, the beach where so many people spend their summer days and the ocean where mystery awaits. She wishes that one day, just one day, she will be reunited with her greatest friend. "Who am I kidding, my wishes aren't going to be true anytime soon" Ashlee thinks to herself. She gets ready to leave the cliffside but then something catches her eye; a figure flying in the sunset sky, a familiar figure. And it's not just Ashlee that's seeing it, she looks down at the beach and sees people pointing towards the sky.
"Eyan" she yells, unaware that a person is behind her. The person in question, a man in a black suit and wearing the sort of glasses prison guards are seen wearing a lot. "Beautiful sight isn't it?" says the man "Um, pardon me, who are you?" asks Ashlee "Agent Hawkins, P.S.A." answers Hawkins "What is P.S.A.?" asks Ashlee "Hmph, thought you were familiar with that sort of stuff. P.S.A. stands for Paranormal Security Agency. An urban legend in some ways, though we are very real" explains Hawkins "Um, no offence, uh, Mr. Hawkins, but you look identical to that guy Rude from Final Fantasy VII" says Ashlee "I do huh. People always comment on that but I never believe them, and that is when I do see people" says Hawkins, looking mildly annoyed "Wait, what do you want?" questions Ashlee "I need to speak with you, about your friend" answers Hawkins "What about him?" asks Ashlee "What happened to him? How did he just disappear? When did it happen? Why did it happen?" says Hawkins "I'm not telling you. I don't trust you, and I don't think I ever will" says Ashlee "Well, in that case, you are committing a felony against the law. I trust that you don't want a police record at sixteen. What would your parents say if I had to tell them that you are refusing to share information with the government? I'm sure they wouldn't mind, or maybe they will say 'Take her away'. What would happen to you if I don't get my necessary information? Listen kiddo, I know that you know that your friend Eyan recently transformed into a flying Pokèmon of some sort, and don't try to sugar-coat it either, it won't end well" threatens Hawkins "First of all, he transformed into a Latios…" says Ashlee "Oh, so now I have actual confirmation that you know" says Hawkins "Leave me alone!" screams Ashlee, running away "Hmm, good try kid, but don't think I won't find you" thinks Hawkins.
Ashlee arrives at her home, desperate to escape the madness that happened earlier with Hawkins. "Hello, Ash" welcomes her mum "Um, hi" says Ashlee as she runs to her room. In her room, Ashlee is trying to figure out what just happened. She feels really uncomfortable thinking stuff like "What if that Hawkins dude finds me" and "I can't keep Eyan's transformation a secret forever". Suddenly, a loud noise is heard downstairs and Ashlee runs down to investigate. Hiding in a corner, she sees men in SWAT gear looking around and her family being arrested by two men in black suits. One of them has a red ponytail and red markings underneath his eyes, the other man is Hawkins. "Listen Miss, um, what's your name?" asks the red ponytail guy "I'm not telling you until I find out what is going on" argues Ashlee's mum "Um, Ryder, I'll take it from here. Tell me where your daughter is now!" yells Hawkins "Um, Hawkins" says Ryder "Not now Ryder. I'm busy" "Dude, their daughter is over there" yells Ryder "You! Come here, thought you'd run from me huh?" screams Hawkins, chasing after Ashlee and knocking over Ryder in the process.
Luckily, Ashlee is fast on her feet, and she makes her way towards the beachside cliff where she has spent much of her days for three weeks. She gets there, thinking that the fall will be safe if she got trapped. Unfortunately, it isn't and she soon finds herself cornered by Hawkins and Ryder. "Listen girl, we only want to talk" says Ryder "Yeah, now you can come along nicely or we'll have to use force" threatens Hawkins. Suddenly, the ground shakes and things begin to fall down. Hawkins' and Ryder's car is crushed and the part of the cliff Ashlee is standing on breaks off and tumbles to the ground. Ashlee falls with it and is crushed by thousands of rocks. "What the hell just happened?" says Ryder, confused "An earthquake! What are you, dumb?" mocks Hawkins "Clearwater Town doesn't get earthquakes" states Ryder "And now, we'll never get the information we need from her, she's dead!" yells Hawkins "Don't say that. If she is who we think she is, more than likely in a few seconds, the rocks that buried her will shatter and she will rise from the pile" says Ryder, now actually afraid "What's the worse that could happen?" asks Hawkins. As soon as he said that, the ground rumbles yet again and the rocks that buried Ashlee shatter. "What, what just happened to me?" gasps Ashlee. A familiar voice communicates with her, one that is nearby "Ashlee, what did I say about following my destiny?" says the voice "Um, don't follow it, follow my own. Wait, Eyan!" cheerfully screams Ashlee "Yes it is me, I'm back but I need you to focus for a second" says Eyan, using telepathy "You're still a Latios?!" asks Ashlee "Of course I am, there's no changing that. Looks like you're in trouble, so I'm helping you. But something must happen" says Eyan "Yes, what, anything?" asks Ashlee, wanting to know "You must become a Latias. And leave your current life behind" tells Eyan "Yes, I will. I've been sitting at that cliff just waiting for your return all day every day since your transformation" says Ashlee, happy about it at the same time "I know, I fly around at sunset" says Eyan.
Eyan touches Ashlee with his forehead and in an instant, Ashlee transforms into a Latias, much more faster than Eyan's transformation and nowhere near as painful. Hawkins & Ryder see the whole thing and get out there shotguns. "If you two freaks take one more step, we'll blow your spirited brains all over the sand" yells Hawkins "And yeah, then we will tell everyone about you both and become famous" says Ryder. Then without warning, both Eyan and Ashlee use Dragon Pulse against the two 'secret agents'. When the two get up, they both see Eyan and Ashlee flying away. Police arrive at the location and after much yelling at Hawkins and Ryder, they arrest them and take them away.
Eyan and Ashlee, the Latios & Latias now fly around the Earth and eventually find a way into the fantasy realm that is now known as the Eden.