You can recruit Articuno in Frosty Forest after beating the game. Recruit rate is 30%.
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Celebi is found at the end of Purity Forest. You don't need to battle Celebi to recruit it.
You can recruit Deoxys in Meteor Cave. Recruit rate is -10%.
One random Deoxys form is created on every floor when the leader enters: Attack, Speed, or Defense. The random Deoxys must be defeated to unlock the stairs down. The Normal Deoxys is on the 20th floor, and it is the only one that can be recruited. After Deoxys is recruited, the player gains access to the Enclosed Island Friend Area, of which Deoxys is the only inhabitant.
Groudon can be recruited in Magma Cavern after you beat the game. Recruit Rate is -10%.
Ho-oh can be recruited in Mt. Faraway. Recruit Rate is 99.9%. Cannot be recruited on the first time the dungeon is completed. The Friend Bow can also be found behind a locked door on floor 30 of the dungeon.
Jirachi is found at the end of Wish Cave. If the player has a Wish Stone, it may grant the player a wish, such as lots of money or a free Friend Area. If the player does not request a wish, Jirachi will offer to join the player's team.
Jirachi will battle you whether you have it or not, but you can only get wishes if you do and recruit it if you don't.
Kyogre can be recruited in the Stormy Sea. Recruit Rate is 50%.
Latios and Latias
After defeating Latios in the Northern Range, he will send the player to Pitfall Valley to rescue Latias. Latias does not fight the player and the two will freely join the rescue team after this dungeon is completed for the first time.
Ho-oh can be recruited in the Silver Trench. Recruit Rate is 99.9%.
Entei can be recruited in the Fiery Field. Recruit Rate is 0.1%. Cannot be recruited on the first time the dungeon is completed.
Raikou can be recruited in the Lightning Field. Recruit Rate is 0.1%. Cannot be recruited on the first time the dungeon is completed.
Suicune can be recruited in the Northwind Field. Recruit Rate is 0.1%. Cannot be recruited on the first time the dungeon is completed.
Mewtwo can be recruited in the Western Cave. Recruit Rate is 99.9%. Cannot be recruited on the first time the dungeon is completed.
Mew can be found in the Buried Relic, and spawns randomly from floor 36-98 if the player has a music box in their inventory. The music box can be created with the parts you get from defeating the Regis.
You can recruit Moltres in Mt. Blaze after beating the game. Recruit rate is 30%.
Rayquaza can be recruited in Sky Tower. Recruit Rate is -10%. Cannot be recruited until after the credits.
Regirock, Registeel, and Regice
They all can be found in Buried Relic. They're recruit rate is 0.1%.
Floors 15, 25 and 35 are a fight with each of the Legendary titans, Regirock, Regice and Registeel. On defeating them, the player will receive the Rock Part, Ice Part, and Steel Part, respectively. Separately, their only use is to be able to recruit the corresponding titan (a function that the Music Box can perform as well). Once all three are obtained, they will join together to form the Music Box.
You must also have their respective parts (or the music box) in your inventory. The Music Box is also used to recruit Mew.
You can recruit Zapdos in Mt. Thunder after beating the game. Recruit rate is 30%.
Hope I helped and hope I got everything!