Pokemon Smaragd

Both Team Magma and Team Aqua are featured as the villainous teams, each stirring trouble at different stages in the game. The objective of each team, to awaken Groudon and Kyogre, respectively, is eventually fulfilled.
Rayquaza is prominent plot-wise, awakened in order to stop the destructive battle between Groudon and Kyogre. It is now the one out of the three ancient Pokémon that can be caught prior to the Elite Four challenge, while still at the same place and at the same high level as in Ruby and Sapphire.