The Elite Four are the last bosses. After defeating them, you face the champion. (In Red, Blue, Yellow, Fire Red, and Leaf Green, this is your rival. Gold, Silver, and Crystal have Lance as the champion. In Ruby and Sapphire, you fight Steven. You battle Wallace in Emerald). The Elite Four from Ruby and Sapphire will be covered here.
To beat them your Pokémon should be at least at Level 55 each. The simplest possible team that can win the tournament comprises four Pokémon: One fire, One Water, One Ice, and One Electric type.
The first of the Elite four is Sidney. He specializes in Dark Pokémon. He starts the battle with Mightyena who will lower your Pokemon's Attack with Intimidate. Mighteyana has Sand Attack to lower accuracy, and uses Crunch and Take Down to attack. Take Down causes recoil damage and might miss. Mightyena also has Roar to scare your Pokemon away but very rarely uses it. Despite Intimidate, Bug and Fighting types should be able to deal with him without too much trouble.
Cacturne has Cotton Spore to lower your Pokemon's Speed by two levels and Leech Seed to suck away some of your Pokemon's energy and restore his own on every turn. Cacturne's signature move is Needle Arm, which is quite strong and has a chance of causing flinching. His final move is Faint Attack so don't bother raising your Pokemon's evasiveness or lowering Cacturne's accuracy. Another thing your should remember about Cacturne is that, despite not being a Rock, Ground or Steel type, he is immune to Sandstorm because of Sand Veil, which makes him harder to hit in a Sandstorm. Bug types should wipe the floor with him.
Shiftry has the same massive weakness to Bug types that Cacturne has. You could also use a Dark type, which is immune to Extrasensory, meaning that Shiftry can only hurt you on the first turn with Fake Out, which causes flinching, or get you to hurt yourself with Swagger, which also increases your Pokemon's Attack by two levels. The really annoying thing about Shiftry is Double Team so you should defeat him quickly before he can use it to dodge your attacks.
Sharpedo has Surf, Crunch, Slash, and Swagger, but the Swagger is a massive risk on Sharpedo's part because his Defence is terrible. However he has Rough Skin, so whenever you attack him physically, your Pokemon will take damage. Fortunately his Special Defence shouldn't be much better than his Physical Defence.
Sydney's main Pokemon is Absol who is a powerful Physical Attacker and has Swords Dance to make him even more dangerous. Despite not being a Flying type, this Absol also has Aerial Ace. Slash is strong and has a good chance of causing a nasty critical hit. Absol also has a unique move called Snatch, which means he literally snatches your Pokemon's stat changes; for example if he uses Snatch and you use a move like Double Team, Absol will Snatch the move and use it instead of your Pokemon. Therefore the only safe way of defeating Absol is to just pound him with powerful, and preferably super effective, attacks.
After Sidney comes Phoebe, a user of Ghost Pokémon. She has a rather boring team, since she has two members of two species, Banette and Dusclops. Admittedly there aren't many Ghost types to choose from in Hoenn, but there is Shedinja so she could have used it. Anyway her final Pokemon is Sableye.
Phoebe's first Dusclops is a stalling Pokemon who has Confuse Ray, Future Sight, Curse and Shadow Punch. Future Sight doesn't work until two turns after it's used and Curse forces her to sacrifice half of her HP. Shadow Punch can't be dodged. Phoebe's second Dusclops, which is also her highest leveled Pokemon, is much more aggressive, although she does know Confuse Ray just like the first Dusclops. Her other moves are Shadow Ball, Ice Beam and Earthquake. Both Dusclops have Pressure forcing you to use up two PP instead of just one whenever you attack them.
The two Banette are at the same level so you won't know which one your facing until they use a move that is not Shadow Ball. One of them has the unique Skill Swap, allowing her to swap her Insomnia ability, which prevents sleep, in exchange for your Pokemon's ability. She also has Toxic, which will cause steadily increasing damage to any Pokemon that is not immune or is not protected by Safeguard, although Toxic sometimes misses. Her last move is Psychic. The other Banette has Spite, which will lower your Pokemon's PP when it's used, Will-O-Wisp, which causes burning and Faint Attack which never misses.
Sableye has a unique typing, unless you include Spiritomb who was not introduced until a Generation later. Being a Ghost and Dark type, she has no type weaknesses. She has Attract to infatuate male Pokemon, and will then use Shadow Ball, Faint Attack and Psychic.
Next up is Glacia, who uses Ice type Pokemon. Her team is even more boring than Phoebe's because she has three members of one evolutionary line, two of them being in the same stage of evolution, and two other members of the same species.
Glacia's first Glalie has Light Screen to decrease the power of Special Attacks for five turns. She also has Hail, Ice Beam and Crunch. The second Glalie has almost exactly the same moveset; the only difference is that she has Shadow Ball instead of Light Screen.
Like the two Glalie both of Glacia's Sealeo have Hail. The weaker one also has Ice Ball, which gets more powerful on each turn, Body Slam which can cause paralysis and Surf which is a strong move. The second Sealeo has Attract, Blizzard and Dive.
Walrein is the only Pokemon in the Hoenn league who can use a OHKO move, which is Sheer Cold. If it hits, and luckily for you there's a good chance that it won't, it will knock out any Pokemon that is not at the same or a lower level and is not Shedinja or a Pokemon with Sturdy. She also has Body Slam, Surf and Blizzard, being the only member of Glacia's team who doesn't know Hail.
Drake, the Dragon Master, is the strongest member of the Elite 4. He starts with Shelgon, who is extremely slow but has Rock Tomb which will cause damage and lower your Pokemon's Speed whenever it hits. He also has Protect to block blows and Dragon Claw and Crunch to attack.
Drake has two Flygon, one of which has Fly and Dig, and is immune to Ground type moves even when he's underground because of Levitate. He also has Dragon Breath, which can cause paralysis, and Sandstorm. The second Flygon has Sand Attack in addition to Flamethrower, Dragon Breath and Crunch. Ice types can deal with both of them but watch out for the second Flygon's Flamethrower.
Drake's Altaria has Dragon Dance to increase his Speed and Attack at the same time. This makes his Take Down more powerful in addition to giving him a better chance of striking first. He also has Refresh, which is pointless since if you cause a status condition, Drake can just recall Altaria so that he heals himself with Natural Cure. His final move is Dragon Breath. An Ice type should be able to knock him out in one hit.
Salamence is Drake's most dangerous Pokemon and will frighten your Pokemon with Intimidate to lower its Attack power. Salamence is, like all of Drake's Pokemon, vulnerable to Ice types but has Flamethrower to hit them super effectively, unless they are also a Water type. He also has Crunch, Dragon Claw and Fly.
The champion, Steven Stone, uses Pokemon that are all immune to Sandstorm, since they are Steel, Rock or Ground types, in Aggron's case both a Steel and a Rock type. Skarmory is his first choice and he can set up a trap with Spikes, but a Pokemon that can fly or levitate can avoid them or you can blow them away with Rapid Spin. Skarmory also has Toxic which can be a problem, in addition to his main move, Steel Wing, and the unavoidable Aerial Ace.
Aggron may look threatening but this particular Aggron is actually rather pathetic. His moveset is dreadful and he is extremely vulnerable to both Ground and Fighting types. His attacks are Solar Beam, which is a pathetic attempt to defend him from Ground or/and Water types, Dragon Claw, which unfortunately is a Special Attack in this generation, Thunder, which is in-accurate and Earthquake, which is useless against Flying or Levitating Pokemon.
Claydol has both Reflect and Light Screen which decrease the power of Physical and Special Attacks for five turns each. It also has Ancient Power, which has a low chance of raising five of its stats at once, and Earthquake.
Cradily is resilient and has Giga Drain to make him even harder to take down. He also has Confuse Ray, which is extremely annoying, Ancient Power and Sludge Bomb.
Armaldo has Aerial Ace, a ridiculous move for a member of his species, Water Pulse, Slash and Ancient Power.
Metagross is Steven's highest leveled Pokemon and can really hurt almost any opponent; the only Pokemon that is completely safe from Metagross is Shedinja thanks to its Wonder Guard. Metagross has Earthquake and Psychic in addition to its signature move Meteor Mash, which might raise its already high Attack power, and Hyper Beam, which forces it to recharge after it's used.
If you are playing Pokemon Emerald, then instead of Steven, you are greeted with Wallace, the old Water-type Gym Leader of Sootopolis City. If you picked Torchic because you thought Steven was still champion, then you have another thing coming.
As a Water type Champion, his Pokemon are all of the Water type. He opens up with a Wailord, level 57, with Double-Edge, Water Spout, Rain Dance, and Blizzard: Water Veil as the ability, so no Will-O-Wisp here. Water Spout works best when Wailord is at full HP, so you bring him down, it's not as bad. Blizzard is another thing to watch out for, but he should go down pretty easily.
Next up is Ludicolo, level 56; Swift Swim for the ability. With Leech Seed, Double Team, Surf, and Giga Drain, this thing likes to raise evasion, seed you, and heal any HP lost on his part. Luckily for you, Aerial Ace is an infinite accuracy move, and Ludicolo is weak to Flying, along with Bug and Poison. You should know what to do from here.
After Ludicolo comes Whiscash, level 56, with Hyper Beam, Amnesia, Earthquake, and Surf: Oblivious for the ability. Whiscash's only weakness is Grass, which was classified as a Special move in that Generation, so Amnesia effectively weakens the moves. Hyper Beam is to scare off any unwanted visitors and Earthquake/Surf are meant for STAB. Tropius is recommended because it resists Surf, immune to Earthquake, and can take a Hyper Beam fairly well.
Tentacruel afterwards, level 55, Clear Body for the ability, with Toxic, Ice Beam, Surf, and Sludge Bomb. This Pokemon screams Anti-Grass, and has a right to. Whiscash is recommended, but any Water-Ground or Water-Rock type will do. Tentacruel has pretty great Special Defense to defend of Psychic types, but mediocre Defense for Ground. Just something to keep in mind.
Gyarados will end the fight really quickly if you're not careful, level 56, with Earthquake, Surf, Dragon Dance, and Hyper Beam, with a few Dragon Dances, Hyper Beam does a large amount of damage if not named Rock or Steel. With Intimidate, Gyarados lowers any Rock type that tries to mess with it. Skarmory does quite well in this situation, but with a few Dragon Dances, Hyper Beam still does a lot. Plan accordingly and he should go down.
Wallace's strongest Pokemon, Milotic comes out, level 58, Toxic, Ice Beam, Surf, and Recover, holding a Sitrus Berry, to add to the pain. Not only is Milotic a pain to bring down, but it's ability, Marvel Scale, makes it so its Defense doubles if Paralyzed, Poisoned, or Burned. This Milotic is almost one you could use on a Stall team, in fact, it works quite well. Not much to say here other than Ludicolo is probably best here, with a resistance to Water and regular damage to Ice, the worst that will happen is that he'll be poisoned and Milotic will spam Recover.
Once you beat Steven/Wallace, you are the Champion in all of Hoenn. Your party Pokémon will enter the hall of Fame and will get a ribbon each. The end credits start rolling in but the game can be continued by restarting the Game Boy Advance.
You can savor your victories in various ways: win the contests and catch the three Regi's if you didn't do that before. Go ahead on the quest to complete your Pokédex.
Latios (Ruby) or Latias (Sapphire) will now roam Hoenn. In Emerald, watch the TV at your home in Littleroot Town and speak with your mother, your answer to the color question (blue=Latios, red=Latias) will determine which one roams. In all three versions, you can acquire the other with the Eon Ticket event item which will take you to Southern Island.
In Mossdeep City, if you visit Steven's house you can pick up a Beldum that he asks you to raise. You can now visit the enjoyable Sky Pillar and catch Rayquaza (Ruby and Sapphire) and Battle Tower or Battle Frontier (Emerald). Also in Emerald, there's another something you might want to know about later...