There was a young child who was going to a school called "Rhode Acadamy". He was getting the best grades in school, and showed a gift for Pokemon, which later turns out to be the ability to talk to Pokemon, as his father's father did, who was the person that helped solve the Pokemon outbreak, since he was the only other person on Earth that was not afraid of the creatures. He goes to a place called "The Starter Garden", which students one-year ahead of him went to to catch their first Pokemon. But he was gifted enough for it. He went their, and was given two things for the capture.
-A Master Ball, to make sure he caught the Pokemon he wanted without fail.
-A Pokemon known as "Pathetikarp", the pre-evolution of Magikarp, that dies if you don't either catch the Pokemon you're facing, or run away (And it has the Runaway ability). If you don't do one of those two, you are sent back to the start and have to try again. After he catches the Pokemon, Pathetikarp dies, since it's life-span is 15 minutes (That's why there aren't any in the other dimension where Pokemon live), and your first Pokemon replaces it in your party (It's over Missingno, so it's not considered a part of your party, you just use it to catch your Pokemon).
Then the child returns to the beginning of the garden, and finds a guy getting attacked by a Bidoof. The student defeats the Bidoof, and goes back into the original building, and is given a TM containing "Vaccum Cut", so you can fight Pokemon even if your starter learns crappy moves.
Then, the student goes into the main building, where there are a bunch of jealous kids that battle him, attempting to make him late to class, even though they lose miserabely. He goes to his Battling class, where he faces his life-long rival, "Casidy Hitler", from a lost family related to an evil dictator that started a war in 1940-ish. She loses, and becomes mad.
Outside, all of the student's friends celebrate and cheer him on, until Cassidy, and her stupid friends, "Beau", and "Steven" come out of the building. They all come at him with their three Pokemon at once, a Trapinch, Slowpoke, and Tyrouge. If the child wins, they run away crying. If he loses, his friend DJ heals his Pokemon and tells them to come at him seperately, and they run away, worried that they might have to do so, because they'd know they'd lose. (Fun fact: if you lose a battle in the school, you wake up in the dorm room, and D.J. tells you you were dreaming. You tell him you had a nightmare about losing a battle, and he mentions that would never happen, so it was just a dream.
The next day, the president shows up at the school, saying he's looking for the student. Out of the huge crowd, he walks toward the president. It turns out the principal contacted the president replying to a letter, where he requests that she joins Team America, which she could not do, but she knew there was a student that was even more capable. The president, the boy, and the principal walk into the school, and go up a secret elevator. As soon as the three come out, the boy realizes that he's in a huge stadium. He fights three trainers, including the principal, to prove his Pokemon capabilities. Of course, he passes.
Then, the president brings him off the campus, and to this airplane. On the plane, he meets a bunch of 16-year-old kids his age, who are the other members of Team America. They say the plane needs to go to California real quick to get some things for the West Division (There are two devisions to Team America, the West and the East. The West is bent on making money and winning, the East is bent on fun, dedication, and teamwork). The two devisions never talk, really. The West has their own side of the plane. However, over the Missouri River, the plane falls to the ground.
When the people get out of the plane, they realize they were by an abandoned engine factory by St. Louis. They go in looking for the source, and a ghost who died on the last plane crash helps the boy get to this room, where there is a strange, shiny stone with the brail equivalent of "Steel" writen on it. As soon as the boy tries to pick it up, a Registeel appears, trying to attack. The Team sedates it, and brings it on the plane back to California, and after, Washington D.C.
At the capital, they examine the strange stone, realizing it has an encription on the back. "The one who gathers the Regi-Runes will be the one to control the ultimate power. The next rune for Treasure hunters' sake is under the legendary streets of the City of Liberty." When a team member named Flag reads this encription, Registeel immediately responds, and the boy captures it. Registeel automatically joins the boy's team. Then, Team America sets off on a journey to find this "Ultimate power", so they can win the World Cup.