The Via Purifico dungeon will be split into two parts, one where you control Yuna and another where you will control Tidus. Upon finally gaining control of Yuna, you will see that you are alone, but that will be but for a brief moment. Move forward and use the Save Sphere as you see fit. Should you get into any battles, you will likely have to summon Aeons to take out the fiends, so get used to it for right now. There will be three paths before you in the first room, but your first goal will be to get some more party members. So, with that in mind, take the eastern path at the beginning and follow it to split. Head north into the room to find Kimahri, as well as a chest that contains a Mega-Potion.
Note: The directions you follow here should always be via the minimap, as the camera will change periodically while moving around.
Continue north and you will eventually reach another room, with Auron in this one. Feel free to use the Save Sphere here to replenish your HP/MP, then keep going to the west. When you reach the T-junction, go south until you reach another room. Venturing east here will not only find you Lulu, but also a chest that contains a Wht Magic Sphere. Return to the room you were just in, then head south until you reach another room. There’s a chest here, with an Elixir inside, as well as a glyph you can touch amongst the rubble. When you exit this room, take the eastern path right out of it to return to the beginning room.
From the starting room, go north and past the teleport glyph. You should see a gate in front of you, but you will be going into the room on the east right before that gate. This room will contain a chest with a Blk Magic Sphere inside, as well as a glyph on the floor. Stepping on this will move the one teleporter from the center room and to the northwest portion of the maze. Leave the room and continue north, to where you found Auron, then head west until you run into the teleporter. The arrows on it will blink twice before changing the direction and you will want to go west on the minimap.
If done right, you should be in a room on the opposite side of the nearby gate. In here, you will find two obvious chests, containing a Lucid Ring and a Skill Sphere. There is one more hidden chest here, right by the gate, so head there and keep spamming the interact button until you open the chest holding 10,000 Gil. Exit the room via the teleporter (make sure the arrow is pointing down), then head to the second Save Sphere again. Feel free to save your game, then take the hallway north of it, where you will run into Isaaru, who was sent to deal with the traitors. Note that you will be fighting Isaaru’s Aeons, three in a row, with only Yuna’s Aeons.
BOSS - Grothia
Despite the different name, Grothia is really just Ifrit, so you will know what to expect. Similar to the Belgemine battles, you cannot use your own Ifrit here, so you will have to choose another Aeon. Also, Grothia will absorb Fire, but he isn’t weak to any of the other elements, so there is no sense in summoning Shiva, unless you want to worry about healing her more often, because of her weakness to fire. At the beginning of the battle, Grothia will have a full Overdrive gauge, so he will use Hellfire. Outside of that, the other attacks he will use are his normal one and Fira; Grothia doesn’t seem to use Meteor Strike at all.
Bahamut is a good choice to use against Grothia, and you should use Shield before his first turn to mitigate the damage from Hellfire. It’s better to not use Impulse with Bahamut, as it causes a bigger delay than the other moves in his arsenal, so stick to the strongest spells, like Thundaga, Blizzaga, or Waterga. Remember to avoid using Firaga, since Grothia will absorb it and you don’t want to make the fight any longer than needed.
BOSS - Pterya
The second Aeon that Isaaru summons is called Pterya, which is Valefor. If your Bahamut is still good after the previous battle, you can use him again here, but if not, Ixion, Ifrit and Shiva are good candidates. Pterya doesn’t have an elemental affiliation, so you don’t have to worry about accidentally healing her. The upside about using an elemental Aeon yourself is that you can use their respective element to heal them, like Shiva using Blizzara to heal herself. As far as what you’ll be dealing with, Pterya has her normal attack and Sonic Wings, which can delay your turn sometimes. There’s nothing you can do about this, but accept it. When her Overdrive is full, she will use Energy Ray, so make sure to Shield when you know it’s coming.
BOSS - Spathi
Isaaru saves the best for last, as Spathi is Bahamut, so you won’t be able to use your own. Despite that, you can use one of your elemental Aeons to battle with Spathi, since they can heal themselves with their respective element. Thankfully, Spathi will not attack normally, as all he will do is count down to Mega Flare, starting with five. So, you can attack like you would normally, possibly avoiding any attacks that might delay your turn. When it is Spathi’s turn and he’s about to unleash Mega Flare, use Shield with your Aeon to minimize the damage. The only time you might want to use your own Overdrive, if you have one, is at the beginning of the countdown.
Upon beating all three of Isaaru’s Aeons, the game will move over to Tidus, Wakka and Rikku, who are in another part of Via Purifico.