Emerald

Pokémon Emerald is the sequel to Ruby/Sapphire and features many new changes.

Major Changes
*Male and female characters have different outfits
*Pokémon are animated when they appear in battle.
*The Battle Frontier 
*Some Traits (like Intimidate and Flame Body) now have effects outside of battle.
*Gym Leaders have new Pokémon and will give rematches after you beat the game. Also, Wallace is the new Champion and a new Leader, Juan, has taken over the Sootopolis Gym.
*All Pokémon Contests are held in Lilycove City. The other Contest buildings have been replaced with Battle Tents (mimicking the types of battles found in the Battle Frontier).
*Both Kyogre and Groudon can be caught in the same game.
*Team Magma now has their own hideout in the Jagged Pass.
*Both the Root (Lileep) and Claw (Anorith) Fossils can be found in the same game 
*Deoxys, Mew, Lugia, and Ho-oh can be caught in game after getting special tickets from Nintendo events.
*After beating the Elite 4, a new section of the Safari Zone opens where players can catch 2nd generation Pokémon unavailable in other versions.
*After completing the Hoenn Pokédex, Prof. Birch will give you a choice of the three Johto starters (Chikorita, Cyndaquil, or Totodile)
*Two in-game trainers can team up together and challenge you to a 2 vs 2 battle.

Game Guides

TM/HM List – Find out where to get all the TMs and HMs in the game.

There are still certain Pokémon you can’t catch in Emerald and have to be traded from other versions.


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Ruby/Saphire

Major Changes
*A whole new land – Hoenn
*Many new Pokémon, bringing the total up to 386
*Many new moves, items, and Berries. Berries can be made into PokéBlocks through use of a Berry Blender.
*2 vs. 2 Pokémon battles
*Pokémon Contests
*Natures (Adamant, Timid, Hasty etc.)
*Abilities/Traits (Blaze, Static, Poison Point etc.)
*Ability to create Secret Bases
*New evil organizations – Team Magma and Team Aqua

However, these two games also deleted some features that were available in previous generations. 
*There is a clock in the game, but it doesn’t show differences between Day and Night and doesn’t keep track of days of the week.
*Can’t access Johto or Kanto.
*Can’t trade with previous generations. That means many Pokémon were unobtainable. This disappointed many fans. 

Game Guides

TM/HM List – Find out where to get all the TMs and HMs in the game.

As with previous generations, certain Pokémon can only be found in Ruby and certain Pokémon can only be found in Sapphire. 
Jirachi and Deoxys cannot be found in any of the games and can only be obtained through a Nintendo even (or a cheating device)

Fire Red/Leaf Green

Pokémon Fire Red and Leaf Green are the remakes of the classic Red and Blue versions. They are included in the 3rd Generation of the Pokémon Gameboy games (also called the Advanced Generation). Many new additions and changes were made since Red/Blue, including most of the changes seen in the previous 2 generations (the new Pokémon, attacks, items etc.)

Major Changes
*A set of 7 new islands accessible after beating the Elite 4These islands have some Pokémon from the 2nd generation, such as Wooper and Sentret. 
*The VS Seeker, which allows you to rebattle trainers 
*The Elite 4 will gain stronger Pokémon after you complete a 
side-quest.
*Move Tutors can teach your Pokémon moves that were previously TMs in Red/Blue versions, such as Swords Dance and Body Slam.
*Players can gather in a Union Room using a Wireless Adaptor, where they can chat, battle, and trade Pokémon.
*Natures (Adamant, Timid, Hasty etc.)
*Ability to play mini-games with other players using a Wireless Adaptor.

There is no clock in these two versions though, so Eevee can’t evolve into Espeon or Umbreon unless traded to Ruby/Sapphire/Emerald.
Also, infamous glitches like Missingno and item duplication have been fixed so they won’t happen anymore. 

The same Pokémon that couldn’t be found in the Red version can’t be found in the Fire Red version, and Pokémon that couldn’t be found in Blue also can’t be found Leaf Green. Also, certain 2nd generation Pokémon are only available in one version.