After beating Giovanni, Red goes through Victory Road and makes it to the Indigo Plato. He used Jolteon, Scyther, Lapras, Persian, Dodrio, and Charizard to face the Elite Four. He used Jolteon against Dewgong, Scyther against Bruno's Onix, Dodrio against Agatha's Gengar, and Lapras against Lance's Dragonite. He had beaten the Elite Four but Lance informed him that there was one more champion left to face. Red discovered that this was Blue. After a speech, Blue sends out Pidgeot and Red sends Jolteon, who presumably defeats Pidgeot. Scyther and Alakazam then battle and presumably knock each other out. Lapras defeats Rhydon, although it wasn't easy. Despite the type advantage, Arcanine defeats Lapras. Exeggutor defeats Dodrio, who is then defeated by Persian. Blastoise defeats both Persian and Jolteon and Red is left with Charizard and Green Blastoise. Just when Charizard is about to lose he defeats Blastoise, shocking Blue. Blue then announces Red as the champion and Professor Oak reveals himself, saying he came to congratulate Green but when he got here he and a Red were finishing the battle. Oak then congratulates Red and enters him and his Pokemon into the Hall of Fame. Red then swears to never let that title down.
Red continues his journey to complete the Pokedex. He uses Persian to capture a Fearow, he catches an Arbok as well. While surfing with Lapras he captures a Tentacool. He goes into the Safari Zone and finds a Chansey. He tries to decide between throwing a Rock or bait at it when it begins to run and a Red chases after it and captures it. Red ventures to capture Articuno using Rapidash, Zapdos using Tauros, and Moltres using Charizard. After doing so he races to Professor Oak's lab to tell him he has captured all 149 Pokemon but found out that Blue had gotten injured. Blue was looking for the last Pokemon (having captured the other 148 Pokemon) and then got crushed under Blastoise with his Pokedex underneath, so it was not recorded. He reveals it used a lot of barriers and Psychic-type like moves. After looking through Red's Pokedex and not seeing it, Blue determines that Red has not completed it, that there is a 150th Pokedex. Despite Blue's protest, as he wanted to catch it as soon as he heals and rebattle Red, Red decides to go battle and capture this Pokemon. While preparing, Oak questions the Gems Red has and Red says that Mr. Fuji gave them to him. While fishing, Red remembers reading about a new Pokemon discovered in South America called Mew and that they created a new Pokemon out of Mew's DNA, Mewtwo. After saying this, Oak says that it was from the diary of Mr. Fuji, who use to be a famous scientist and tried creating a Pokemon. Oak also says that the large stone was reacting when near Charizard and suggested to have Charizard hold one and Red hold the other. Mr. Fuji hears of Red going to face Mewtwo while feeding Vulpix. He says he doubts Red will win. Red surfs on Lapras and sees Mewtwo. Red then sends out Gengar and challenges Mewtwo. Mr. Fuji says there is only one way to defeat Mewtwo, with those stones he gave a Red. Meanwhile Mewtwo defeats Articuno, proving that even a Legendary Pokemon can't beat it. Red then sends out Charizard and after the battle, they are sent into the waters bellow. Red is about to give up but sees Charizard still ready to fight and decides to continue with him. Suddenly the stones begin to glow and Charizard evolves into Mega Charizard X. Mega Charizard defeats Mewtwo and Red captures it. After the battle, Charizard changes back to it's original form and Red returns home. Red, Blue, and Oak are all eating when Red realizes that there is one more Pokemon to catch... MEW! (Who flys outside the window and winks)
- Type advantages are basically thrown out the window.
- No one is guarding the cave unlike the games.
- Red does not visit the Sevii Islands or rechallange the Pokemon League.
- Blue is not injured in the games, as this is added for dramatic effect.
- The Mega Evolutions are not in any of the original games.
- Red had captured 113 Pokemon prior to battling the Pokemon League and 150 after completing the Pokedex.
- It can be presumed that Persian, Lapras, Jolteon, Dodrio, Scyther, Gengar, and Charizard are Red's strongest Pokemon. Charizard was Red's first Pokemon and uses him in battles, Lapras, Persian, and Jolteon appear frequently throughout the special, Scyther was used in the Pokemon league, and Gengar was brought to fight Mewtwo (although it may also be because of it's type advantage).
- Blue's (Green's in Japan) team is Blastoise, Rhydon, Arcanine, Exeggutor, Pidgeot, and Alakazam, just like the Video Games.
- Blue mentions capturing all but one Pokemon, but seeing as Red captured the Legendary Birds, that means Blue has captured at least two or all of the "Legendary Birds" meaning that they aren't so Legendary.
- Arcanine is never shown to be defeated.
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