When you enter Cleyra Forest Oracle Kildea will offer to show you around the place. Take the tour if you would like to. When she is done giving you the tour you will go back to the beginning of Cleyra. Head up the stairs and open the hidden chest to the right for a Phoenix Pinion, if you move into the area to the right you can find 970 gil behind the sign. Head up the steps and go towards the right. Continue moving along the path and go up the set of steps that you come to. You can buy some equipment from Dan if you want, talk to him and see if there is anything that you need, just don't buy the Thunder Gloves because you can find them somewhere in Cleyra. I suggest buying all of the new equipment for Freya including her Partisan.
Search by the bushes by the stairs to the right for a remedy. Now head into the Inn that is in the middle of this area. Search in the top left corner for Echo Screen, search between the barrel and the chest for 1250 Gil and head up the stairs and search by the cabinet for an Ether. Talk to Mopli and save your game, he should also have a letter from Ruby to Zidane. Move down the stairs on the bottom left below the level with the inn. Search near the sign for Thunder Gloves, climb up the stairs and you can buy some medicinal items from Star Maiden Nina. Search by the mushrooms to Nina's right to get a Phoenix Pinion.
Climb up the steps, you are now in the cathedral area. Search by the right of the cathedral to get an Echo Screen then go into the cathedral. Search by the doorway to the left to find a Yellow Scarf. If you didn't have one of these before equip it to Quina so s/he can learn the Millionaire ability, which allows your party to receive more gil for winning a battle. Don't take to the two Cleyrans yet, leave the Cathedral and search by the entrance into this area to get some Gysahl Greens. Now go back to the area that has the giant sand pit by the entrance to Cleyra. Talk to Quina in this area and when you fall down open the two treasure chests to get Silk Robe and Magician Shoes.
Jump down off the branch and now go all the way through this part again until you get back up to Cleyra. I know it's a long way but just run from the battles and you should be fine. Once you are back in Cleyra, proceed to the Cathedral and talk to the two Cleyrans guarding the entrance. Go back down to the Inn and Soldier Dan will come up with some news. Follow him down the stairs and back to the area with the sand pit, a battle commences.
This battle is quite easy thanks to Vivi's Blizzara Spell. Just keep casting this each time it is his turn and this boss will be dead in no time. Antlion has a variety of damaging attacks and status effect inflicting abilities. One of his attacks called Sandstorm deals damage to the entire party and inflicts Darkness on each of them, unless the have a Guard against it. This can be quite fatal and if he uses it heal all of your characters using potions and cure their negative status ailment by using Echo Screen.
Attack normally with Freya and Zidane, you can also try stealing some items from the Antlion but with Vivi casting his spell you probably won't have enough time to get everything.
After the battle, watch the events and dialogue that take place. Once you gain control of Freya climb up the steps at the top left and go into the Cathedral. Talk to the High Priest and he will give you an Emerald. Now go back to the Inn to find Stiltzkin, talk to him and buy his combo. Talk to Mopli and check Mognet, he has a letter from Monev. Once you are ready go down and meet up with your party at the entrance of Cleyra. Now is a good time to equip your characters with some new equipment if you have any.
Follow the path until you run into the Alexandrian Soldiers. Continue along moving through the areas and fighting the Alexandrian Soldiers. Once Freya and Zidane realize what is going on your party will rush back to Cleyra. Things aren't looking too good, as you arrive back to Cleyra you will get into a battle with a Black Mage. Move to the right to find Stiltzkin, talk to Mopli and he will give you a letter to deliver.
Leave this area and attempt to climb up the stairs and you will enter a battle with three Alexandrian Soldiers, after this battle you will fight more Black Mages. Choose the 'Let's head right!' option when you are prompted with the choice. Follow them up the steps and tell the Burmecian family to go left. Another battle a couple of Alexandrian Soldiers and a Black Mage will commence. When you reach the waterfall guide the family to the right and yet another battle with some soldiers will begin. Tell the family that they are not safe yet when you are prompted with the choice.
A sequence of dialogue and events will take place. Eventually the conversation will be interrupted by Beatrix. Before chasing after her talk to the Cleyrans and Burmecians that you saved, each of them will give you items. You will receive a Nymph Card, an Ether, a Phoenix Pinion, a Zuu Card, an Elixir, a Phoenix Down and a Remedy if you saved all of them. Talk to Mopli to save your game and use a tent, take the time to equip your characters with better equipment if you haven't done so previously.
Exit the Cathedral and you will have to fight Beatrix, again!
Start off the battle by having Freya cast Reis's Wind and Quina casting Mighty Guard if you have it. If you have the Bandit ability equipped to Zidane it shouldn't be hard to steal all of the items that Beatrix is carrying. Cast Slow with Vivi on Beatrix. Alternate between regular attacks and stealing for Zidane and Jump and normal attacks with Freya. Beatrix uses a variety of damaging attacks, be ready with Quina to heal your characters if they need it.
Quina should be there to heal your party members and revive them if they are KO'd. Just like with the last battle with Beatrix, she will use Stock Break when you have spent all of her HP which will reduce all of your character's HP to 1 and end the battle.
Once the party finds its way out of Cleyra, watch all of the events and dialogue until you gain control over Zidane again. Your party is now aboard the Red Rose, Queen Brahne's Airship. Follow the moogle into the last screen, this is Serino and you should have a letter for her from Mopli. When you are done move down and back to the first screen and join your party.