Mystery Dungeon - Bosses

Mystery Dungeon has several major battles throughout the story. Most of them are against Legendary Pokémon such as Zapdos and Articuno.
This guide is going to help you fight off these enemies.

Team Meanies

Your first important battle is against Team Meanies (Consisting of Gengar, Medicham and Ekans). Though this isn't a legendary battle, it's a battle you can't avoid.
First off, you're going to want to combat these Pokémon with moves that are effective against them. For Gengar, it is good to use Psychic, Ghost or Dark type attacks. For Medicham it's best to use Flying and Ghost types and Ekans is most damaged by Ground and Psychic types.
But don't fret if you don't have any of these type attacks. They shouldn't be hard to beat anyway. xD

Zapdos

Zapdos is the first legendary battle you will face. It is located on the 13th floor (Or the 3rd floor of the Peak) of Mt. Thunder.
Like all the battles, it is best to use attacks that are super effective against the opponent. In this case: Zapdos, being an Electric/Flying type is affected by Rock type attacks, though Ice types to get at its Flying type will work too.
Zapdos cannot be recruited into your team at this stage. You must wait until the end of the game and come back.

Moltres

The second legendary you'll face is the fire bird, Moltres. It is located on the 13th floor (or 3rd floor peak) of Mt. Blaze.
Again, playing to Moltres' weaknesses is the key. If you chose a water type starter, you're in luck. Moltres is most affected by Water and Rock type moves. The occasional Electric attack wouldn't be too bad either.
Moltres won't join your team just yet. Come back after you've finished the story and maybe it will.

Articuno

The final of the three legendary birds, Articuno, is located on the 15th floor (or 5th floor peak) of Frosty Forest.
Articuno is weak against Fire, Electric, Steel and Rock type attacks, so try and use those whenever possible.
Articuno, like the others, won't join your team yet. You'll have to go back and try again after you've completed the story.

Mankey Trio

This may not seem like a Boss, but you do have to defeat them in order to continue with the story. The three Mankey are located on the 10th floor of Uproar Forest.
You shouldn't have many troubles, but if you do, go for their weaknesses. Being Fighting types, the Mankey's will be hurt most by Flying and Psychic moves.

Groudon

This battle can get quite hard if you're not using the right Pokémon. Groudon is located on the 25th floor (or 3rd floor peak)
Being a ground type, Groudon is severely hurt by Water type attacks. Grass and Ice type attacks would do some damage also.
Groundon won't join your team after this battle. Go back after you've finished the story and he just might.

Rayquaza

The final boss in the game; Rayquaza is on the 34th floor (or 9th floor Peak) of Sky Tower.
To ensure this battle goes perfectly smooth, you're going to need to use Ice Type moves. (Chances are you don't have any Dragon moves, but if you do, they'd help too.)
This will be the toughest battle yet. Rayquaza has a whopping 600HP to whittle down. To have little troubles, your team should be averaging level 40. If they aren't, go train in the Makuhita dojo for a while. The Dragon Room gives off a lot of experience points.
After you defeat Ray, that's the end of the main storyline! Congratulations!