Emerald also makes gameplay changes that are connected to the story and other areas of the game like its post story content. With both their goals of awakening Groudon and Kyogre respectively realized, it falls on the player to awaken the legendary Pokemon Rayquaza to cease the other two Pokemon's battle. In Emerald, both Team Magma and Team Aqua are the culprits. Pokemon Emerald takes all the information from its predecessors and proceeds to set up its own unique story. In short, Emerald takes the foundation that Pokemon Ruby and Sapphire provided and then tears it down for a near complete remodel.

The game makes large strokes with how its main story is done, both in its conflict and the conclusion, alters large swaths of post-game content, and unifies certain aspects of the Hoenn region that were divide in the original Ruby and Sapphire games. It begins to make more noticeable changes to Gen 3 in several different ways. Like every generation of Pokemon games, both Pokemon Ruby and Sapphire share similarities with only minor differences, something that changes with the series’ release of Pokemon Emerald. This can be anything from individual Pokemon and their evolutions to story aspects to how whole areas of the game are approached. Much like the first two generations of Pokemon games, Gen 3 has aspects that are version exclusive to each of its individual titles. The third generation of Pokemon games, Pokemon Ruby, Pokemon Sapphire, and Pokemon Emerald, all feature a lot of similarities but stand out from each other with quite a few differences.

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