When you arrive back in Muse with the Entry Permit, Nanami will hand out roles for the party to play to trick the guard into believing they are Alex, Hilda, and Pete. During the scenes, choose any selection you like, as they all result in the same thing: a night in jail. The party will spend the night in the Muse jail, with Viktor and Flik bailing them out in the morning. When released, take Viktor's advice and take Pilika to stay with Leona at the tavern.
Before you do ANYTHING: this is very important. Not only is it vital to recruiting a character, but missing a one-time chance item as well. Head south down the path by the blacksmith and you will be stopped by a woman. She will ask you for a favor, and then give you a Two Packages item and leave. Keep going south and Clive from the original Suikoden will ask you if you've seen the woman; your answer doesn't make any difference. When he leaves, try to exit Muse, and Elza will show up to take the Packages from you and hand over a Sound Set #1 item. Clive will confront her and Riou will be caught in a crossfire between the two, before Elza escapes with Clive on her tail. If you do not see this scene, which has an extremely limited time to view, not only will you be unable to obtain the Sound Set #1 item elsewhere in the game, but Clive will not join your party later on either. When you've seen this scene, head to the Muse City Hall to continue the game.
Inside, Viktor will take you to meet the mayor of Muse, Anabelle. Watch the scenes, where you learn some of Riou and Nanami's grandfather's past, and follow Jess inside the storeroom. He needs you to infiltrate Highland's camp at the border to find out the state of their provisions. He will give you two Highland Uniforms and it is suggested you return to the tavern to take some others with you.
Before leaving, check the bookshelf that is the furthest back in the room for the Old Book Vol. 4. This IS a missable item as the times you can enter the city hall are extremely limited. Get this now or you will likely not have a chance to obtain it again.
On your way back to the tavern, you will likely see an old friend, Tuta, hanging around near the center of town. Talk to him and inform him of what became of the Mercenary Fortress. He'll take you inside to meet Dr. Huan and then will join your army.
After Tuta joins, go back inside the house and talk to Dr. Huan to obtain Recipe #3. This is also a missable item and needs to be acquired as soon as possible. Once the events involving Muse are over, you cannot obtain this item again.
I wish this guy would tell me where he got his Prosperity Rune. The method to acquire this rune, much later, requires some tough decisions. When you return to the tavern, choose your party members, and the next destination is the Muse-Highland Border, but first, a few more new recruits.
Before attempting to recruit Anita, you should head over to the item store and buy some Antitoxin; you may not need, but do so anyway. Talk to her several times and she will present a set of choices to Riou. Either to get Leona to refill her drink, give her an Antitoxin, or complement her on being a beautiful swordsman. After fulfilling a request, leave Muse, and return to talk to her again to get another request. Keep doing this until she asks what you really want from her and you can ask her to join your party; which she will. Our next stop is all the way over to the burned Mercenary Fortress.
At Viktor's old Fort you'll meet Templton, the cartographer from the original Suikoden. Watch the scenes and then follow him to Toto Village. Find him on the east-side of town and tell him that you are fighting the Highland Army and he will join your army. Like usual, he will also hand over the Suiko Map special item which will allow you to see a mini-map of the world when out on the world map. Extremely useful. When Templton has joined, make sure your party is ready, and look for the Muse-Highland Border which is to the northeast of Muse.
Talk to the soldier when you arrive and follow him to the entrance of a shortcut through the forest that will lead you to the outskirts of the Highland camp. Just a small note that this is a one-time dungeon and you will be unable to return here later, so make sure to grab the chests; none of which are hidden.
The enemies in this small dungeon are not much to note, except you may want to look for the Armadilloid. This rather rare encounter drops an excessive amount of potch when defeated. You can also use a character with a Technique Rune on their weapon to steal even more potch from them. If you are wanting to stock up on Fury Runes in Muse, this is a great way to make money. When you reach the edge of the forest, Riou and Jowy will change into their Highland Uniforms and infiltrate the base. The tent you want is in the northeast side of the camp, with the soldier guarding it. Riou and Jowy will fumble their way inside of the tent, but will be confronted by their old captain, Rowd, as they try to escape with the information on the provisions.
Before escaping, grab the treasure chest outside the tent that had the previsions in it to obtain the Fire Sealing Rune. This rune will make you invulnerable to fire damage, but doubles your damage from water attacks. The water element is scarcely used in this game (Although the final boss does have a water-elemental attack), so this rune can be quite useful. The best use of this is to put it in one of Zamza's rune slots to make his Fire Dragon Rune deal no damage to himself when used. You can also use this in conjunction with the Fire Lizard Rune on your weapon to take no fire damage from it; at least until you can get a Rage Rune to replace it. To continue the story, enter the large white tent on the west-side that looks different from the rest. You will meet the Princess of Highland, Jillia, here. Watch the scenes, then exit to the south to attempt to leave the camp.
Jowy will attempt to hold off Rowd and the Highland soldiers in order to allow Riou and Nanami to escape. Make sure to select the "......" selection to Nanami; this is very important! Choosing this option will allow you to get into a steady battle with Highland soldiers, of which hold your only chance to obtain an item in the game.
The Highland soldiers here are the only place in the game you can acquire the Silence Rune. It is highly recommended that you keep fighting the soldiers here until you obtain one. The rune itself, isn't very good, but once you leave this area, there is no other way in the game to obtain it. When attached to a weapon, it gives a chance to inflict the silent status effect on an enemy. This can have a place against some bosses that use runes, but for normal encounters, it's of little value. Afterwards, leave the forest and return to Muse, without Jowy, unfortunately...
In Muse, try to enter Anabelle's room to talk with Jess in city hall and you will be denied entrance. Visit Leona's tavern and Viktor and Flik will join your convoy and force themselves into the room. They are thankful, but unable to do anything about Jowy. Disheartened, the party will return to the tavern. Follow Nanami to the gates of the city to wait for Jowy. When prompted, always choose to stay and wait with her, and then Pilika. Finally, Jowy will return.
In the morning, your destination is Jowston Hill, in the northwest part of town, but first, Jowy is, unfortunately, about to leave our party for good. It's important that you remove all of his runes and equipment now that you want to keep. At the conference, Flik and Viktor will join your convoy. Watch the scenes that unfold between the members of the City-States here.
Back at the tavern, Anabelle will ask Viktor to stall the Highland Army while awaiting for reinforcements from the State. Make sure to save your game before you engaged in the battle. There is a recruit that is missable in the next army battle.
In this battle, like the last few at Viktor's Fort, it's a matter of turns before it ends. The important thing is that the mercenary, Gilbert, that is fighting for Highland, is a Star of Destiny. In order for him to join your army, he MUST be damaged (One sword in him). 9 times out of 10, Flik's first move will be to use the Fire Spear on Gilbert, wounding him. If this doesn't happen, you will need to hope that this occurs during the next turn. If Gilbert is killed before joining you, or the battle ends before he switches sides, you will permanently miss him! Once he switches sides, he has joined you, and if his united is defeated, as long as you don't get the message that he was killed in battle, it is of no consequence. As for the battle itself, you can do whatever you like. I would recommend moving Riou's unit just barely north enough to use Bright Shield to heal Gilbert's unit once he switches sides. Other than that, let the NPC units battle it out. The battle ends the turn after the Matilda Knights retreat.
After the battle, talk with Nanami and you will find Jowy talking with a mysterious man in the corner of the other room; whom should be familiar if you played the first game. In the morning, this is your absolute last chance to shop here, get Recipe #3 from Huan, and the Old Book Vol. 4 from the city hall storeroom. When you are done, visit Anabelle's room in city hall, then return to the tavern. When Jowy leaves, follow him out to near the corner of the entrance to city hall, and he will again, be talking with Kage. That night, return to city hall to talk with Anabelle...
You'll find that Jowy has betrayed you, and killed Anabelle. As she dies, she will apologize for what the State had done to their grandfather, Genkaku, and die in peace knowing that they were happy being raised by him. Jess will enter to find Anabelle and announce that Highland has invaded the city. There are random encounters out on the streets with Highland soldiers, but nothing you shouldn't be able to handle with just your two characters. Head for the tavern to pick up Pilika, and the next morning, south to the town of Coronet to continue the story.