Location: Petalburg Woods

When you reach Petalburg Woods, you willencounter a grunt who is harassing a Devon Corporation employee. You step in to defend the scientist and the grunt will then leave, with you getting a Great Ball as thanks.

When you leave the Woods, a strange grunt will report back that they have sported a trainer who shows promise.

Location: Rusturf Tunnel

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 Parts, 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.

Location: Slateport City

Your next encounter with Team Magma/Aqua is in Slateport City. At first, you will see them blocking the entrance to the Oceanic Museum. When you go to the harbour to look for Captain Stern, you will be told that his is in the museum and that opens up. When in the museum, you will have to battle two Team Magma/Aqua grunts who want to take the Devon Parts.

After defeating them, then Maxie/Archie will appear and introduce themselves, noting that you have fierce determination. They will note that they have plans to change the world and that you may help shape it. He then leaves without battling you, warning you to stay away.

In Route 110, you will then see some grunts who will inform you that they are heading to Mt. Chimney.

Location: Meteor Falls

As you reach Fallarbor Town, you will encounter your rival who will inform you that something terrible has happened. She will take you in to meet Professor Cozmo's wife who informs you that the team has abducted Professor Cozmo

When going through Route 114, your rival will appear and note that the professor has been taken to Meteor Falls. Go there and you'll encounter an admin for the team who will challenge you in a tag battle.

Magma Admin Tabitha	Mightyena	Numel
Items	Level 23	Level 23
	Intimidate Quick Feet	Oblivious Simple
	Attacks: Odor Sleuth Roar Snarl Swagger	Attacks: Magnitude Flame Burst Amnesia Lava Plume
	Hold Item: No Item	Hold Item: No Item

Aqua Admin Shelly	Mightyena	Carvanha
Items	Level 23	Level 23
	Intimidate Quick Feet	Rough Skin -
	Attacks: Odor Sleuth Roar Snarl Swagger	Attacks: Aqua Jet Assurance Screech Swagger
	Hold Item: No Item	Hold Item: No Item

When you have defeated them, then the other team shall appear and introduce themselves, saying they intend to stop them.

Location: Mt. Chimney

Following the Meteor Falls incident, you have to follow the teams to Mt. Chimney. Now some grunts are no longer blocking the Cable Car in Route 112, you can take it up the mountain. When there, you will encouter grunts from both teams, as well as the leader from the other team duking it out. Get to the end, facing off against grunts and an admin, and you'll encounter Maxie/Archie over the volcano with the Meteorite. They're trying to use the Meteorite to gain the power to merge with the planet's core to awaken Groudon/Kyogre. They explain about the Primal Reversion and then challenge you.

Magma Admin Tabitha	Koffing	Numel
Items	Level 24	Level 24
	Levitate -	Oblivious Simple
	Attacks: Assurance Clear Smog Sludge Self-Destruct	Attacks: Magnitude Flame Burst Amnesia Lava Plume
	Hold Item: No Item	Hold Item: No Item

Magma Leader Maxie	Mightyena	Golbat	Camerupt
Items	Level 25	Level 25	Level 27
	Intimidate Quick Feet	Inner Focus -	Magma Armor Solid Rock
	Attacks: Roar Snarl Swagger Assurance	Attacks: Wing Attack Confuse Ray Air Cutter Swift	Attacks: Flame Burst Amnesia Lava Plume Earth Power
	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item

Aqua Admin Shelly	Grimer	Carvanha
Items	Level 24	Level 24
	Stench Sticky Hold	Rough Skin -
	Attacks: Disable Sludge Mud Bomb Minimize	Attacks: Aqua Jet Assurance Screech Swagger
	Hold Item: No Item	Hold Item: No Item

Aqua Leader Archie	Mightyena	Golbat	Sharpedo
Items	Level 25	Level 25	Level 27
	Intimidate Quick Feet	Inner Focus -	Rough Skin -
	Attacks: Roar Snarl Swagger Assurance	Attacks: Wing Attack Confuse Ray Air Cutter Swift	Attacks: Assurance Screech Swagger Ice Fang
	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item

Location: Southern Island

When you get to Route 118, you will meet Steven and, shortly afterward, Latias/Latios will appear and inform Steven that there is an issue on Southern Island. When you get there, you will find Latios/Latias and soon after encounter another Team Magma/Aqua Admin who is trying to take the Mega Stone for Latios/Latias. When you refuse, they will challenge you in a tag battle where you're teamed with Steven Stone.

Magma Admin Courtney	Camerupt
Items	Level 31
	Magma Armor Solid Rock
	Attacks: Lava Plume Earth Power Curse Take Down
	Hold Item: No Item

Aqua Admin Matt	Sharpedo
Items	Level 31
	Rough Skin -
	Attacks: Swagger Ice Fang Scary Face Slash
	Hold Item: No Item

Location: Route 119

When you get to Route 119, you will find the Weather Institute. As some grunts are blocking the path beyond it, you have no choice but to go in. When inside, you learn that Team Magma/Aqua have taken over and are trying to learn about the way that the ancient Pokémon affected the weather. Once again, the admin at the end will challenge you.

Magma Admin Tabitha	Camerupt
Items	Level 32
	Magma Armor Solid Rock
	Attacks: Lava Plume Earth Power Curse Take Down
	Hold Item: No Item

Aqua Admin Shelly	Sharpedo
Items	Level 32
	Rough Skin -
	Attacks: Swagger Ice Fang Scary Face Slash
	Hold Item: No Item

Location: Mt. Pyre

Following the Weather Institute fiasco, you will encounter some grunts who note that they are heading to Mt. Pyre. When you reach the ssummit, you will see the grunts. At the top, the leader, Maxie/Archie, will take the Red Orb/Blue Orb from the pedestal.

Magma Admin Courtney	Camerupt
Items	Level 38
	Magma Armor Solid Rock
	Attacks: Earth Power Curse Take Down Rock Slide
	Hold Item: No Item

Aqua Admin Matt	Sharpedo
Items	Level 38
	Rough Skin -
	Attacks: Ice Fang Scary Face Slash Poison Fang
	Hold Item: No Item

You then take the Blue Orb/Red Orb and have to follow the team to Slateport City, where they will steal the submarine Captain Stern has created and take it to their base

Location: Team Magma Hideout/Team Aqua Hideout

Your next encounter with the teams are in their hideouts in Lilycove City. When you get there, you have to face through a variety of grunts and navigate lots of teleportation puzzles in order to proceed. At the bottom, in the dock, you'll have to face off against a horde of Team Magma/Aqua Grunts. At the end, you will find Courtney/Matt in front of the submarine telling you it's too late as they're heading for the Seafloor Cavern

Magma Admin Courtney	Camerupt
Items	Level 39
	Magma Armor Solid Rock
	Attacks: Curse Take Down Rock Slide Yawn
	Hold Item: No Item

Aqua Admin Matt	Sharpedo
Items	Level 39
	Rough Skin -
	Attacks: Ice Fang Scary Face Slash Poison Fang
	Hold Item: No Item

Location: Seafloor Cavern

You won't be able to make the next encounter until after Mossdeep City Gym. When you leave the gym, a large burst of energy will come out of the water and into the sky. This is Team Magma/Aqua breaking the seal of the Seafloor Cavern. Steven will give you Dive and request that you go investigate

When you get in there, you have to navigate the cavern until you come to the end where you encounter Maxie/Archie. They will challenge you in one final battle, this time with Mega Evolutions

Magma Leader Maxie	Mightyena	Weezing	Crobat	Camerupt
Items	Level 41	Level 41	Level 41	Level 43
	Intimidate Quick Feet	Levitate -	Inner Focus -	Magma Armor Solid Rock
	Attacks: Scary Face Embargo Taunt Take Down	Attacks: Haze Double Hit Sludge Bomb Explosion	Attacks: Poison Fang Mean Look Acrobatics Haze	Attacks: Curse Take Down Rock Slide Yawn
	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item	Hold Item: Cameruptite

Aqua Leader Archie	Mightyena	Muk	Crobat	Sharpedo
Items	Level 41	Level 41	Level 41	Level 43
	Intimidate Quick Feet	Stench Sticky Hold	Inner Focus -	Rough Skin -
	Attacks: Scary Face Embargo Taunt Take Down	Attacks: Sludge Wave Screech Venom Drench Gunk Shot	Attacks: Poison Fang Mean Look Acrobatics Haze	Attacks: Scary Face Slash Poison Fang Crunch
	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item	Hold Item: Sharpedonite

After defeating, Tabitha/Shelly comes up to Maxie/Archie to try to stop him from awakening Primal Groudon/Kyogre for it is the end of the world. Using the Red Orb/Blue Orb, they will awaken Groudon/Kyogre who will unleash harsh sunlight/severe rain on all of Hoenn, and Steven recommends you head to the Cave of Origin to calm them. Meanwhile, the Admins chastise the leaders of the Team for being reckless and causing the end of the world

Location: Sootopolis City

Heading to the Cave of Origin, you will encounter both teams outside the Cave of Origin in Sootopolis City. To try and make up for things, they will give you the Magma Suit/Aqua Suit in order to survive and wish you well as you go to confront Groudon/Kyogre.

After you have calmed them down, they will thank you for your help and resolve to change their ways and rebuild the team to do things properly.

Location: Petalburg City

During the Delta Episode, you will hear of someone stealing Key Stones from various people across the Hoenn Region. You will learn from your rival that there is trouble in Petalburg City. Go there and you will encounter Courtney/Matt attacking Wally, asking for his Key Stone. They will challenge you and then leave as Wally's Key Stone has already been taken.

Magma Admin Courtney	Camerupt
Items	Level 53
	Magma Armor Solid Rock
	Attacks: Rock Slide Yawn Earthquake Eruption
	Hold Item: No Item

Aqua Admin Matt	Sharpedo
Items	Level 53
	Rough Skin -
	Attacks: Poison Fang Crunch Agility Skull Bash
	Hold Item: No Item

Location: Rustboro City

Later in the Delta Episode, you will go to Rustboro City. When there, if you go to Devon Corp, you will hear a load of noise going on. You will encounter the scientist from earlier in the game and have to defend him against several Grunts. You will discover that Team Magma/Aqua have stolen a special device that Devon Corp have been making called the Link Cable. He will then tell you that the team is heading to Mossdeep City.

Location: Mossdeep City

Go to Mossdeep City and you'll bump into Courtney/Matt and some grunts as they go to the Space Center. Enter and you get a horde battle with the grunts who have five Mightyena with Intimidate. Go upstairs and you'll face Courtney/Matt who wish to bring an end to the world. You battle them and a Grunt at the same time. They have a Mega Evolution

Magma Admin Courtney	Camerupt
Items	Level 55
	Magma Armor Solid Rock
	Attacks: Rock Slide Yawn Earthquake Eruption
	Hold Item: Cameruptite

Aqua Admin Matt	Sharpedo
Items	Level 55
	Rough Skin -
	Attacks: Poison Fang Crunch Agility Skull Bash
	Hold Item: Sharpedonite

Defeat them and Zinnia appears and steals the Link Cable. She destroys it and then steals Courtney/Matt's Key Stone and leaves to grab one more from the Team Magma/Aqua Hideout

Location: Team Magma Hideout/Team Aqua Hideout

Go to the hideout and the grunts will say that Zinnia is too powerful but luckily their leader is deep in the base. You have to go through it again, battling various grunts. Reach the office and you'll see Zinnia facing off against Maxie/Archie and his admin Tabitha/Shelly. They have lost to Zinnia and Zinnia soon spots you and mentions you're the hero and here to save the world again, but saying you're too late, stealing Maxie/Archie's Key Stone and says that they can now summon Rayquaza and says that she hopes you can follow her. She leaves while Maxie/Archie gives you the Cameruptite/Sharpedoite respectively.

This is the last encounter you will have with the team of your game, but you can visit them in the Hideout at any time and battle with the leader in the Battle Maison.

Location: Battle Resort

When you arrive on the Battle Resort, you'll meet up with the opposite team's leader and admins who will congratulate you on stopping the issues and imagine how easy it could have been them that you had to stop. They then give you the Sharpedoite/Cameruptite respectively in your game.