Unfortunatly, Kefka, finds you, forcing you to escape on Chocobos, while Figaro goes underground. From there upon your escape the town of South Figaro is next. There meet up with Sabin to have him join your party. Defeat the boss Vargas, join the Returners, and Barron will join the party.
On the river, defeat the boss Ultros, the from here the part slpits its ways, Locke goes to South Figaro, there have Locke initially steal the merchant's clothes, then have him steal the soldiers clothes. If you want the special item cider, beat up the two merchants to acquire the cider. Celes will join the party, and steal the clock key. To defeat the boss Tunnelarm, using the Thunder Rod helps.
In the other mission, with Sabin and Shadow, enter the Imperial base. Find the Doom Train, which you might recognize from FFVIII. There you can have a ghost enter your party, just ask the right one. After you defeat the Spectre the ghost will die, from there go defeat the Doom Phantom Train. Shadow will leave your party, which leaves you a man shorter to beat the piranhas, but Gau will save you.
To have Gau join your party, you need to do a few things first. That is to purchase some dried meat, and when you see him in battle instead of striking Gau, give him some of the dried meat(Mobliz) then he will join the party.
From there the journey brings you to the Serpent Trench, which will in turn take you to Nikea.
Upon getting on the ship sailing to South Figaro, the second mission will be complete.
With Terra, Barron, and Edgar, go to Narshe, and once there, make sure to talk to the old man, Arvis. Kefka will attack Narshe, and after defeating his troops, your alternate party will come to scare him off. Following his departure, Terra will fly away as an esper.
Travel south to Jidoor. There you can rent a chocobo for 250 gil, which is a fast way to get you to Zozo. At Zozo you will find Terra, and Ramuh the esper. Edgar's chainsaw, and four more magacite can be found as well. Also to save you some much valuable time from messing with all of the clock combinations, the right time is 6:10:50.
Next is the Opera House, so make sure you read the script as it will help you very much. Saved Celes, from the baddie, Ultros. Go to Albrook, meet up with Cid, then defeat the boss #128. After a battle with the cranes, Terra will tell her story. Use the airship, to go to Maranda, from there you can purchase the magicite Sraphim, at Tzen.
Upon going back to Narshe, Barron and the Narshe elder will devise a plan against the empire. If you lose Mog at this point, do not worry, you can get him back at a later time. From Narshe, make way to the Imperial Base, but it will be abanded. Then the goal on hand is to find the sealed gate of the espers.
Depending on what you say to emperor Gestahl, depends on what you will recieve in return from him. I happened to get the second highest score, getting South Figaro, Doma Castle freed, and a Tintabar. Also make sure that you get the Imperial Base opened up as well, since there is plenty of bounty inside waiting to be taken, with your greedy little paws.