Just as in previous games, Pokémon Ruby & Sapphire puts you up against an antagonizing gang of thugs who want to use Pokémon to meet their goals. This time however it isn't Team Rocket, but in a new twist one of the rivaling Team Magma or Team Aqua, depending on the version. They either want to use Groudon to expand the land masses to give more room for land Pokemon, or use Kyogre to expand the oceans to give more room for sea Pokemon. In both cases the opposite team serves a supporting role to you in the story.
Depending on the version too the teams use different Pokemon. In the case of Team Magma, they use more Fire-types such as Numel. In the case of Team Aqua, they use Water-types like Carvanha. Both teams use certain Pokemon though, like Zubat.
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| Encounter #1: Petalburg Woods |
Details:
Like Team Rocket, the teams are shown engaging in petty crimes before their master plan is revealed. Your first encounter with them is in the Petalburg Woods, where a low level grunt is harassing an employee of the Devon Corporation. The assailant takes flight after you beat them. You are given a Great Ball for your troubles.
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| Encounter #2: Rusturf Tunnel |
Details:
Later you meet the same grunt holding the old man Mr. Briney's Wingull hostage in the Rusturf Tunnel. After beating them and retrieving the Devon Goods, you are introduced to the head of Devon and asked to take them to Slateport City's Captain Stern, along with a Letter to be dropped off to Steven Stone in Granite Cave.
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| Encounter #3: Oceanic Museum |
Details:
Next you meet the team in Slateport City, who are at first blocking the way into the Oceanic Museum. Go to the harbour and talk to a man who will tell you to take your Devon Goods to the Oceanic Museum and the members will have migrated inside, where you find them to be giving the good captain a hard time. After you finish off two of the grunts, you will get to meet the team's sinister leader, who will not battle you just yet.
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| Encounter #4: Meteor Falls |
Details:
Your next meeting is in the mysterious Meteor Falls, where you will find the team of your game with one Professor Cozmo, who they have duped into giving them the Meteorite. They will take flight to Mt. Chimney, the local volcano, for more shenanigens. Luckily the opposing team will come to your aid and offer you their support for future meetings.
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| Encounter #5: Mt. Chimney |
Details:
Now the teams are taking their plot more seriously and attempting to use the volcano as a means of realising their goals using power drawn from the Meteorite. The other team will show up to help but is still hopelessly outnumbered. However, this gives you the chance to fight your way through grunts to where the leader of your villainous team is at the northernmost point for your first battle encounter with them. First up is their admin, however, who are a cut above the grunts:
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| Magma Admin Tabitha |
Numel | Poochyena | Numel |
Battle Type
Single Battle |
Level 20 | Level 20 | Level 20 |
|   |   | | | Ruby Only
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 | | |
| Aqua Admin Matt |
Carvanha | Poochyena | Carvanha |
Battle Type
Single Battle |
Level 20 | Level 20 | Level 20 |
|  | | | | Sapphire Only
| Then, your first fight with the leader. They are far stronger than the admins so be prepared:
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| Magma Leader Maxie |
Mightyena | Golbat | Camerupt |
Battle Type
Single Battle |
Level 24 | Level 24 | Level 25 |
| |   | | | Ruby Only
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| |  |
| Aqua Leader Archie |
Mightyena | Golbat | Sharpedo |
Battle Type
Single Battle |
Level 24 | Level 24 | Level 25 |
| | | | | Sapphire Only
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| Encounter #6: Weather Institute |
Details:
The team in your game takes over the Weather Institute on Route 119 and forces all the scientists into a tiny room on the top floor, demanding information on the weather's influence on certain Pokemon. They also will not let you pass the bridge to Fortree City. Defeat these rascals once again to remove them and get a special new Pokemon, Castform.
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| Magma Admin Courtney |
Numel | Mightyena |
Battle Type
Single Battle |
Level 28 | Level 28 |
| | | | Ruby Only
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| Aqua Admin Shelly |
Carvanha | Mightyena |
Battle Type
Single Battle |
Level 28 | Level 28 |
| | | | Sapphire Only
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| Encounter #7: Mt. Pyre |
Details:
On your way to Lilycove City you will spot a handful of grunts muttering something about the ethereal Mt. Pyre and take off in that direction. You are to go up there and find out what they're up to, and if you defeat the stationed guards will see their leader steal either the Red Orb (Ruby) or the Blue Orb (Sapphire) from Elite Four Phoebe's grandparents on the top of the mountain. You are given the opposite orb. They take off for Slateport City for what's next.
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| Encounter #8: Aqua / Magma Hideout |
Details:
There is no battling to be done back at Slateport, but what happens here is essential to the story. In a spectacular entrance, the team of your game steals a submarine off Captain Stern's team and heads back to their hideout in Lilycove City.
If you haven't gone to Slateport yet you will find access impossible to the interior of the base. Likewise, there is a grunt training a pod of Wailmer that prevents you from heading out to the sea unless the Hideout is stormed. Navigate through to the final room of the Hideout (and make sure to find the Master Ball!) to encounter an Admin. After defeating them they proclaim that Maxie or Archie has taken the submarine they stole to underwater near Sootopolis to enact the final stages of his plan. You will require Dive for what's next.
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| Magma Admin Tabitha |
Numel | Mightyena | Camerupt |
Battle Type
Single Battle |
Level 32 | Level 32 | Level 32 |
| | | | | Ruby Only
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| Aqua Admin Matt |
Carvanha | Mightyena | Sharpedo |
Battle Type
Single Battle |
Level 32 | Level 32 | Level 32 |
| | | | | Sapphire Only
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| Encounter #8: Seafloor Cavern |
Details:
After getting Dive and beating the Mossdeep City gym, you must go down deep underwater on Route 128. There you will find the underwater entrance to Seafloor Cavern, where a legendary Pokemon is said to wait. The submarine is parked out near the surface point of the underwater cave, which you must go and explore. Through the rapids and Team grunts you will eventually come to the end of the cave, where the final battle with the Team leader takes place and the nightmare of awakening a brutal weather-controlling legendary Pokemon begins.
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| Magma Admin Courtney |
Camerupt | Mightyena |
Battle Type
Single Battle |
Level 38 | Level 38 |
| | | | Ruby Only
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| Aqua Admin Shelly |
Sharpedo | Mightyena |
Battle Type
Single Battle |
Level 38 | Level 38 |
| | | | Sapphire Only
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|  | |
| Magma Leader Maxie |
Mightyena | Crobat | Camerupt |
Battle Type
Single Battle |
Level 41 | Level 41 | Level 43 |
| | | | | Ruby Only
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| Aqua Leader Archie |
Mightyena | Crobat | Sharpedo |
Battle Type
Single Battle |
Level 41 | Level 41 | Level 43 |
| | | | | Sapphire Only
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Next you must go to Sootopolis City and meet up with Steven. Enter the Cave of Origin to commence the encounter with the Legendary Groudon or Kyogre.
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