This is a mix of the game (not manga, sorry) and anime. The game characters will most likely have a made up personality if they weren't really given one (Red, for example).

AN: Blue = Male. Red's rival. Leaf = girl (who may appear later) This is going to have some popular ships happen & a little bit of crack. But, I'll mostly stay toward ships that are mostly liked. Which ones? Well, stick around and find out.
EDIT/WARNING: Sorry I've forgotten to say(since I had no room in the summery) that this will have BL(Boys Love) Straight, and a tiny bit of GL(Girls love?) too. So if any of that disgusts you, then you might wanna leave.
_

It was the start of a new school, of Poke Oak High and Prof. Oak was excited to see all the energetic and young students' excitement in the halls. Misty, Dawn, May, and Iris ran up toward Ash once they saw him. All were eager to see him and tell them about what has been happening with their travels. Ash was excited to see them all, but there was someone in particular that he wished to see… A lot of girls were surrounding the grandson of the great professor Oak.
"Gary you're so amazing!"
"I love you Gary!"
"Who's Gary? This is Blue!"
"What? Who's blue?" Then there was a big commotion going on, while Gary just sighed and left. He felt this school a complete waste of time for him. After all, he was a great Pokémon researcher and has a good brain on his shoulders. The only reason he'd think this place wasn't so bad is if he were here. Gary noticed another commotion going on.
"Professor Oak only had one son, and that is the great Blue Oak!"
"Blue? That is a stupid name!"
"Hey!"
"Why would someone name their son Blue? Professor Oak's children would never think of such a dumb name like that!"
"How dare you insult the name of the great Blue Oak!" Gary sighed and ignored them. "Some people…" he thought. Then the bell rang, signaling one minute till class. Everyone started scrambling toward their classes, except for Gary. He slowly strolled toward where he is supposed to be.

"Quiet! Quiet everyone!" The history teacher, Mr. Surge shouted at the class. "Just because it's the first day of class doesn't mean you can act like a bunch of wild animals!" May sighed. This class is crazy. This Blue kid, everyone was what everyone was getting so worked up about, and May doesn't get it. He just seems like a stuck-up punk to May. Also, why does it matter if she doesn't know good history like she's 'supposed to?' She's a great coordinator and basic knowledge isn't going to help her any. May sighed and decided to just write a note to Ash on how she feels about him. That seemed more productive to May then to listen to some grouchy guy go on and on. So, while he was explaining school rules, punishments, and what is needed for class, May got out a pencil and paper and began to write. After words, she quietly passed it on to Red, who she thought was Ash. He was right behind her, so she didn't need to make too much of a scene. She wanted to sit next to him, but it seemed some girl and Misty beat her to the punch. But they were their first, and it really wasn't such a big deal to her.

Red took the note and looked at her with a confused look. Things day has been quite odd for Red. People he doesn't know has been talking to him like they were old friends and now Misty sitting next to him reminiscing about things he's sure he has never done with her before. Luckily a good friend of his, Daisy was next to him. Now the girl right in front of him just passed him a note. He looked at Daisy with a puzzled look.
"Well, I guess you should see what it says…" she whispered. Slowly, Red opened it up.
"Now Red, since you find that piece of paper more important than my class, why don't you read it to the class?" Surge asked.
"What? Red?" both Misty and May shouted. Than May put her head on her desk and put her arms around her head and whined, "Oh no…"
"Red, now!" Surge demanded.
"…I rather not," Red said. He already has read the note and found it quite awkward already.
"Then give it to me!" Surge grabbed it out of Red's hand.
"I'm gonna be sick!" May shouted. She then grabbed all her stuff and ran out the room.
"I didn't say you could leave! You're getting an absent on your attendance today!" Surge yelled after May. Then he turned to the class after clearing his thought and read the letter to the class.
"Dear Ash,
I've missed you all these years! Did you miss me? I never stopped thinking of you, and I'm glad we have gotten this chance to see each other again! All these years I've felt strongly toward you, but was just too stubborn to admit it, even to myself. But now I know I there is no need to be, since you're such an amazing and sweet guy. I hope you feel the same. Please tell me if you do after this class.
Love, May." The whole class was laughing while it was being read aloud. Misty wasn't paying attention since she was still shocked on how he wasn't sitting next to Ash this whole time. "But he looks just like him!" Misty thought. Red tried looking out the window and tried to pretend that he didn't hear anything.
"Now for roll call. When I call your name, let me know where you are."

Ash was in PE. His class was running a circle around the gym.
"Man, it's the first day and we have to do this?" Ash whined. Richie was running with him and he said,
"Come on Ash! You can handle this. This is nothing compared to what you used to do, right?"
"Yeah you're right!"
"Come on you wimps! You've wasted so much time as it is!" Chuck shouted.
"Hey, I'll race yea!" Ash said.
"You're on!" Richie said. James was panting and groaned as he saw those two speed up. For some reason, people thought he didn't have enough knowledge and was forced to be a student here too.
"Man, this guy is so hard on us. I wonder how Jessie is doing… Probably better than me," James thought. Worse part is, Jessabelle's here too, and still pursuing him. Iris narrowed her eyes at James and said, "Seriously? Such a wimp." She then focused on Ash and Richie racing. "Go Ash!" she silently cheered. They both finished at the exact same time.
"Great job you two!" Chuck said. Richie and Ash smiled at each other while panting. Everybody else finished. Then Chuck went on about something totally unrelated. The bell finally rang and everyone rushed out the class. Out in the halls, there was a bunch of chatter, and once Ash came out, there was a lot of attention on him.

Jessie ran up to him and couldn't stop giggling. Ash stared at her with an annoyed look.
"What is it?" he asked.
"I was in a class with your friend May," Jessie said.
"So?" Jessie tried to calm herself of the giggling but it was no use.
"Oh, nothing. Just one of your sweet girlfriends wrote you a confession note!" Jessie then busted out laughing.
"A confession note?" But Jessie had left to find James to tell him.
"I think she means a love confession," Richie said.
"Oh phew… I thought May did something to m- What?" Ash shouted. Everyone was now gossiping.
"Is there a problem Ash?" Richie asked.
"I had no idea…"
"Oh I see," Richie said. "Not surprising," Richie thought. "So if you don't mind me asking, do you like this girl May?" Ash crossed his arms and sighed.
"Well…" Iris spied on Ash with a worried look.
"Oh no… What if I'm too late?" She liked Ash a lot, and she was going to tell him after school. But what if she waited till she was too late?
"Well, if she does get him, she better treat him right," Iris silently said. With that, she slowly walked away.

Meanwhile, Red was just minding his own business when Blue popped up.
"What's with these people? They've been arguing over who I am and then you got some g-!" Blue stopped talking when he noticed a guy that looked a lot like him. So much like him in fact, that it was more than just a convenience. Red just looked at the man who caught Blue's attention. He wondered if this is the Gary Oak that the people here where talking about. But he couldn't believe that his grandfather was thee Professor Oak. There was only one grandson the Professor he knew had. Right now, Red had forgotten about the whole letter incident. All the people around them saw Blue and Gary and were now chatting away.
"Wow! There are two of them?"
"How can that be?"
"Well at least there is more Gary to go around!"
"You mean Blue?" The whole commotion went up again. Gary was putting stuff away in his locker and was paying no mind to Blue. He really just wanted to get this over with and get out of here. Most people here are annoying and he still doesn't get why he is here. Blue walked up to him with a glare and said, "Hey, are you copying me?"