You will not be able to access Baaj Temple until you have the airship towards the end of the main story. Once you do, go to the Search function on the navigation controls, and search around (X: 15, Y:55) or so to find the location, which will be added to the list. Travel to that destination and jump into the water, then swim towards the only exit shown on your map to meet up with an old friend.
BOSS - Geosgaeno
The first time you fought this boss, you only had Tidus and weren’t able to actually do much of anything to it. This time around, however, you will be able to finally bring it down. Depending on when you do this and how much you’ve improved your characters, this could be a challenging battle, due to some of the boss’ quirks. Remember that since you’re underwater, you will be forced to use Tidus, Rikku and Wakka for this boss. At the beginning of the battle, Geosgaeno will use Stone Punch to attack a character. This has a chance to Petrify, which is really dangerous, as petrified characters underwater will instantly shatter and be lost for the rest of the fight.
You can protect yourself by equipping armor with Stoneproof on it. Once the boss goes below half health, he will add KO Punch to the mix. This move will alway inflict the Curse ailment (no Overdrives), as well as possibly instantly KOing a character. After the boss attacks three times, it will swallow a party member and on spit out the character on its next turn, provided the character just defends. This will cause the character to only have one HP left, with the other characters taking damage equal to that character’s current HP, minus one. So, if they had 3,001 HP left, the other characters would take 3,000 damage.
The inhaled character will have a Trigger Command while inside Geosgaeno, which is to Struggle. If they do this, then the character will be exhaled and be instantly KO’ed. You do not want to defeat Geosgaeno while a character is inside it, as this will cause it to spit out the character and deal 9,999 damage to the entire party, which is a game over if they don’t have Break HP Limit. It should also be noted that Geosgaeno will take on whatever buffs/ailments (most of them, at least) the character has when they are swallowed. It will not swallow a character if they have Doom.
As already mentioned, Stoneproof will help against Stone Punch, as will Death Ward/Deathproof against KO Punch. If your characters are powerful enough, they can defeat the boss before it has a chance to swallow someone. You could also cast Hastega on everyone to make sure they get more turns. Geosgaeno is weak to all elements, so you can blast it with magic or have an Elemental Strike weapon equipped.
Once you’ve defeated Geosgaeno, search opposite the entrance to the temple to uncover a hidden treasure chest that contains Lulu’s Celestial Weapon, the Onion Knight. You won’t be able to see the chest in the little area, so just keep pressing the X button until you witness Tidus opening it. There is another reason you came here, but it requires obtaining all of the Destruction Sphere treasures from the various temples. If you didn’t get the ones in Besaid or Macalania, you will be forced to fight two Dark Aeons before you can re-enter those temples.
If you did get all six treasures already, then enter the underwater temple and go into the main room. There will be three statues on either side of the room, as well as a large glyph blocking the way to the Chamber of the Fayth. If you have gotten each Destruction Sphere treasure, interacting with each statue on the sides will cause a different glyph to appear. Note that there are two chests in this little room, in the southwestern and southeastern corners, containing four Mega Phoenixes and a Megalixir. Once all of the statues are lit up, you can head into the Chamber and earn a new Aeon, Anima. You’re now done with Baaj Temple.