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This story starts off with an unassuming young man who is about to become a Knight of Gaien.  He and his friends (Tal, Keneth, Paula, Jewel and Snowe) are just about to undertake their Graduation ceremony in their hometown of Razril. 

Once the final challenges of the Marine Academy are over and the celebration is too, the young hero (as he will be referred to) sets out on his first missions.  He along with Snowe, who is actually his captain and a couple of his friends start out with menial tasks such as patrol and messanger duty.  Very soon however, the hero and Snowe are given a tougher task of escorting a merchant to the Island of Illuya.  That merchant is named Mr. Ramada.  The merchant and his underlings seem like shady characters.  The Commander of the Knights, Glen Cott, sent Snowe as the captain, even though he didn't have full competency in his abilities.  Therefor when a ship thought to belong to the pirate Brandeau is spotted, Commander Glen makes way after their ship.

When the Pirate Brandeau catches Capt. Snowe's ship and fire, young Snowe panics and gives the order to retreat leaving the merchant ship to the Pirates.  The hero takes command over Snowe and Snowe escapes into one of the lifeboats.  While Snowe is being picked up by Commander Glen and scolded, the hero is Captaining the Gaien ship against the pirates.  The pirates board the ship and are overcome by the Gaien Knights.  The Pirate Brandeau, unknown to the Knights, is the bearer of the true rune known as the "Rune of Punishment."  He unleashes it, killing everyone onboard except himself and the hero.  He even killed his long time friend and underling, Peck (known as "assassin" in Suikoden IV).   The hero and Brandeau begin a duel that ends in Brandeau's death.  Commander Glen comes just in time to receive the Rune of Punishment from Brandeau. 

The Rune of Punishment (along with his vice-commander, Katarina)  keeps Commander Glen bedridden once he returns to Razril.  Snowe tries to get back into the Commander's good graces.  When pirates attack as a retribution towards the death of Brandeau, the Knights come out victorious.  After the fight, however, Snowe chases after them solo.   The hero is forced to go to his aid.  This as well led to the hero actions being admired by Glen and Snowe's actions being reprimaned.

After the pirates defeat at Razril, they return in greater numbers.  Numbers that are too overwelming for the Knights of Gaien.  Commander Glen is forced to use the Rune's awesome power to stop the pirates.  He does so, but at a great cost. 

When the hero goes up the spire to check on Commander Glen, he receives the Rune of Punishment from him.   Immediatly after, Snowe comes up the stairs and sees Commander Glen die and then vanish.  When the hero received the Rune, he was made unconscious.    Here he has a vision of sort of a man talking to his son, Rakgi.  He is woken up by people talking in the nearby hallway.

It seems that Snowe had mistakenly (or perhaps, purposly) put the blame of Commander Glen's death on him.  He is believed and Katarina comes in to tell him that he is being banished from Razril.  

At this point, two of your friends, will come escort you to the ship where you are sent off into the middle of the ocean.  You are left onboard a small vessel with (supposedly) no oars and few supplies.  You are saved by the fact that two of your friends believed so much in your innosence, that they stowed away on your exile ship.  They are going to stay with you until your name has been cleared of the charges.   Also onboard is the merchant cheipoo.  He stowed onboard the ship trying to get to another island or trading town.  He had the bad luck to pick an exile ship. 

By some luck, the ship eventually gets picked up by a merchant ship.  The merchants will soon to be the Kooluk commanders, "Colton" and "Troy."   Troy is the man of legends surrounding the defeat of Gaien ships in the past.  They are allowed to escape by Troy, because they seem to be of no threat to the Kooluk.  

The crew, after a run-in with a rather nasty sea-creature, get crashed upon a deserted island.  During their attempt to make suitable repairs to the exile boat, the hero runs into a mermaid and attempts to befriend it.  His attempts pay off as before they leaves she alerts you to the danger that the ever-hungry Cheipoo has gotten into.  Cheipoo has to be rescued from a large crab that attacks him for trying to eat the little crabs on the island.  To penetrate the shell of the crab, the hero has to use the Rune of Punishment, once again.  After the fight, he again passes out and has a vision.  This time the vision is of a little boy who wants to taste his fathers bread again. 

When that episode is finally over, the group say goodbye to the mermaid and head south in search of land.  Their luck once again runs cold, when another set of sea-creatures attacks them and causes them to lose their oars.  Once again they are without hope.

As luck always turns around, theirs finally does.  This time they are picked up by a vessel from the Kingdom of Obel.  Their luck turns out much better this time around as they are treated well and returned to the King of Obel, Lino En Kuldes.  

Lino and his daughter, Flare, seem very interested in the Rune of Punishment.  They insist that it was once on this very island.  The king says that there is someone deep in the local ruins that can tell them much about the Rune, but he doubts any of the news will be good.  

After the meeting with the King, you are told that you can live there in Obel, and sent with a man named Desmond to see your new home.   The fact that their home is inside a cave, dissuades the group at first, but the interior turns out to be quite large and beautiful.   Desmond then passes on a message from the King:  Your job for the king will be to gather people together.   He doesn't exactly say why, but he does say that the hero is in charge of it.  

The first order of the business for the hero, was to find the person in the Ruins and find out about the Rune of Punishment.   That person turns out to be a woman named Rikie and her son named Rakgi.  The man from first vision was her late husband.  It seems he once held the Rune of Punishment, just as the hero does now.  She tells the hero of the Rune's destructive ways of killing its wearer.  She admits that since you have the Rune, that her husband is truly dead.  She joins with you so she can be near the Rune. 

The King and Desmond will soon thereafter send the hero after someone he has heard about from Nay Island.  The man is named Oleg.  He has invented a way to see thing that normal people cant see.  What he has invented is called a camera.  He and the hero will use it overnight as a test, and will happen to catch the destruction of nearby Iluya Island. 

The hero rushes back to Lino En Kuldes with Oleg in tow.  The King sees that the Kooluk are about to invade the southern islands.  Right after the meeting with Oleg and Lino En Kuldes, the hero is attacked by the merchants they had escorted earlier.   Mr. Ramada and his underlings, Mizuki and Akaghi, as it turns out are assassins under the employ of a man named Graham Cray.  He had hired them to kill the hero and bring the Rune of Punishment to him.  Once beaten, the King tells them how they were betrayed by Cray.  Mr. Ramada asks to join your movement, and the King agrees, warning the hero to deal with them if necessary.

Very soon after the assassins failed to kill the hero, Kooluk begin an invasion of Obel.  What they hadn't counted on, however, was the craftiness of the Obel King.  He had secretly built a large ship that could house large numbers of people.  This ship is actually the building that the hero was staying it. 

Upon the arrival of the Kooluk, the hero and the princess, Flare, scouted the town of Obel for anyone willing to go.  After recruiting several people, the hero returned to the ship, and Flare decided to stay with her people.  Upon hearing this, the Kings loyal servent, Setsu, left to be by her side.  The King, the hero and many others, took out to surprise the Kooluk with their surprise escape. 

When the time was right, they blew the side of the island out, letting the hidden ship out of the cave, and circled around the Island away from the Kooluk.  Given the option, the Kooluk decided to take the city instead of following after the ship.  Obel is now liberated by the Kooluk.

Following the escape from Obel, you are flagged down by a pirate named Kika, who insists you follow her to her island.  There, an alliance is formed between your group and the pirates to deal with the Kooluk invasion and Graham Cray. 

To deal with the Kooluk and Graham Cray's trading company, the Pirate Dario suggests talking to a woman named Elenor Silverberg.  The pirate Kika sets up a meeting.  Before they  can meet her, though, they are attacked by the Kooluk's Anti-Pirate brigade, as captained by none other than the hero's old friend, Snowe.  Snowe is defeated and chased to Razril.  You also learn that Razril has been occupied.

Once at the dock in Razril, Snowe is denied to land by the citizens of Razril and declared a traitor.  The hero comes up behind Snowe and sentances him to exile.

When theyare finished with Snowe, the group finally gets to go meet Ms. Elenor.  Once at Elenor's house on Hermitage Island, the hero and several of Kika's pirates are drugged by Ms. Elenor's pupil, Agnes.    When Ms. Elenor learns of Graham Cray's involvement she decides to help, but not before sending the hero on a test to prove his determination.

When she boards, her first order of business is to determine the hero as the leader and form an actual army out of the group.  Elenor declares her plan to be one of unification.  She wants to unify the smaller islands and then take over the bigger islands, leaving the Kooluk with no foothold on the island nations.

The first island on their list was Middleport.  The Lord of that island had managed to keep it out of Kooluks hands.  Upon arrival, they are attacked by a large sea-monster that Cheipoo mistakes for an island.  After they defeat it, they learn from the Lords son, Reinbach III and his servent, Micky that the large creature was actually the Lords pet, named Daisy. 

Reinbach III sets the hero up for a meeting with his father.    During this meeting Reinbach II lets it be known that he does business with the Cray Trading Co. and cant help him to fight them.  He does however let the group have free access to his Island and its citizens.   Reinbach III is so upset with his fathers dealings with Cray that he offers to come and help the hero.

Ms. Elenor's plan then leads them to Na-Nal Island.  As soon as the group lands, they are met by Kooluk Soldiers.  After they beat up some Kooluk soldiers, they were arrested by Axel, the son of the Island Chief. What appeared to be an occupation at first turned out to be a coolition.   Na-Nal didn't fall to the Kooluk, they sided with them.  

The Hero and Lino En Kuldes (along with a couple other members of the group) were arrested and charged with the beating of Kooluk soldiers.  The slimy Island Chief decides to let the group perform a favor for him, instead of serving jail time.  He sent them to the local Elven settlement to steal a potion that the Elves were known for.  Unwillingly, they were forced to perform the theft. 

While Axel was escorting the hero and his army back to their boat, an Elf named Selma stopped them and asked them to follow her (at swordpoint).  They were unknowingly led  into a jailcell and are again imprisoned.  The Elven Elder let on that he knew about the burglary and that he allowed it to begin with. 

The group was tricked however, and the Elves had switched the potion for poison.  The Island Chief had then unintentionally poisoned the Kooluk.  The Kooluk immediatly began to slaughter the island people.  Upon finding out what happened, the elf, Selma, rushed back to the cell the hero was in and released him to go back to the people.  For this she was banished and soon joined the hero's cause.

After the Kooluk were stopped, the Island Chief felt betrayed by the Kooluk and decided to go in with the hero.  To show his support, he sent his son, Axel to fight with Hero.

After the events at Na-Nal, they headed over to Nay Island to do negotiations with the Island chief there.

Along the way, a strange thing happened.  A ship appeared out of nowhere.  It was first believed that Nico, the lookout, wasn't doing his job and let an enemy get to them.  It was soon appearant that this was no ordinary ship.  The hero and a couple of his collegues were led onboard the ship to talk to the master of the ship.  The master of the ship, the Fog Ship Guide, wanted to take the hero's Rune of Punishment.  In return he would let him stay on his ship and live forever.  The hero refused and it angered the Fog Ship Guide.  When it attacked, the man who guided the hero onboard decided he wanted to leave as well.  He helped the hero fight off the Fog Ship Guide.  After that a mysterious figure named Leknaat, came and told the guide that it didn't belong here. 

The man, who's name is Ted, was the owner of another True Rune, called the Souleater.  He had given it to the Guide 150 years ago.  When the Guide was gone the Rune returned to him.  He soon joined the hero, although, very reluctantly.

 Once the group got to Nay Island, there wasn't much by way of resistance.  Once the Island chief learned that Lino had given his proof of Kingship up, he understood the gravity of the situation.  The only help he was able to offer was a couple of survivors from Iluya.  He offered it without much hesitation.

With Nay Island, Middleport and Na-Nal Island taken care of, it was time for the hero and his friends to go back to Razril.

When the Kooluk invaded Razril, there was no help or reinforcements sent from Gaien.  Because of such, it was unknown if Razril would be taken back for Gaien or not. 

As the army approaches Razril, there is a heated naval battle.  They were successful in defeating the Kooluks occupying Razril and even got the leader to switch to their side.  They also acquired one of their ships.

They landed in Razril, and quickly began to gather as many citizens together as they could.  Even though they had defeated the Kooluk in a naval battle, there was still a war going on.  Hero made a speach that many citizens of Razril could get behind.  Following this, the former lord of Razril, Vincent Vingerhut, came to the hero and tried to arrest or kill him and his party.  Upon failing that, he tried to sell the island to the people.  The citizens of Razril quickly ran him and his bodyguards off.  Several of Razril's citizens joined the the hero's army, most notably the two friends the hero had left behind. 

Upon leaving Razril, the hero is once again thrown into a naval battle with Snowe.  Hero wins easily and again sentances Snowe to exile.

A man named Pablo, who had been with the army since their HQ had became mobile, told the Hero of a man who might be a great help.  This man was named Warlock, and was suppose to know a lot about Rune Cannons. 

The hero went to check on this rumor.  As he was told, he found Warlock underneath Middleport at the back of a series of underground caves.  Warlock was an elderly man who did indeed know much about Rune Cannons.  He knew they were evil, and he wouldn't help Pablo study them.  He joined to help end the war.

The next step was to take Obel back.  The plans for that attack didn't occur in the War Room as is normal.  They went to the Nest of Pirates.  While there, the hero returned the Golden Seal to Lino En Kuldes, as requested by Ms. Elenor.  Both she and Kika suggested that he no longer needed it to be a great leader.  The plans to retake Obel were no different than any other island, The battle would just be a little different.  

Without anything to stop them, they headed straight to Obel.  The split their ships into two in order to pinch the Kooluk.  Hero led the charge straight on, while Kika led the attack to blindside them.  They defeated the Kooluk and managed to capture its captain, Colton.  It is then revealed that Elenor had used Flare on the island to take over a ship that Colton had planned to use against you.  It was hidden in the cave where the HQ was once held.

Very soon, however another fleet would appear.  Hero and his army were thrown right into another naval battle.  Although this one was different. The ships (Colton identifies them as the governor's privateer fleet) did not fight back.  They just took all of the army's cannon fire.  The trick came when they were set ablace and heading straight towards the hero's ships.  It was a trap concocted by Graham Cray.

With opposition from everyone except Elenor, Hero used the Rune of Punishment once again.  This destroyed the fleet that was going to take them down with it.  However, once again Hero was thrown mentally back into the bizarre tunnel.  Here he would see Commander Glen's shadow.  Glen would be impressed by his strength.

Once Obel is liberated, the army finds many new recruits. 

Most interesting happens when a trading post hint led them to a man floating aimlessly in the water.  This man would turn out to be Snowe.  He at long last accepts the Hero's invitation to join. 
He started off the child of the lord of Razril and a Captain.  He sold out his citizens and sided with the Kooluk.  After he was defeated by the hero outside the Pirates Nest, he fell out of favor with the Kooluk.  In desperation, he put together a crew and began pirating.  He would once again be beaten by the Hero outside Razril.  Following this, he would be left to die by his pirate crew until found by the hero.  He was the last person recruited by Hero before the siege to Fort El-Eal.

Mr. Ramada, who had a shady past, had managed to make himself very useful to the hero.  He would often go out spying on the Kooluk trying to get more information.  At Fort El-Eal, he was capture, but not before finding the governor imprisoned by Graham Cray.  He was able to get information on the fort's defenses from the governor and relay it via his pet bird to Hero.  From this information, Elenor begins her strategy for taking on Fort El-Eal.

To stand a chance against Fort El-Eal, they had to first deal with the giant Rune Cannon that had destroyed Iluya.  To do this, they would use a second fleet.  These ships were steered by mermaids until they got within reach and they were abandoned by the mermaid sisters.  The Kooluk fired their giant Rune Cannon, which takes a couple hours to reload.  During this time, a group of hero's comrades landed in fog at the base of Fort Al-Eal.  As they made their way through a near deserted Fort El-Eal to dismantal the Rune Cannon, the main fleet charged in for a naval battle with Troy, the child of the sea god.

The group (led by Elenor, herself) made it to Graham Cray.  A battle broke out, and they were ultimately victorious.  Cray, however wasn't dead.  He had just ran off.  Elenor stays behind while the rest of her group clear a path out.  She takes care of the Rune Cannon and then goes to look for Cray, her old apprentise. 

Hero wins his battle with Troy's fleet, then heads up Fort El-Eal, as well.  Eventually they find themselves at the very top of the fort.  It is here that they find Cray and he describes his purposes.  He has manipulated the whole war, looking for the Rune of Punishment.  He will make Hero fight the great tree, hoping it will kill him so he can acquire the rune.  When the tree is defeated, the hero's group has to evacuate before the fort falls down on them.

Elenor then appears with Graham Cray and shows simpathy for him.  Neither are seen again.

When Hero makes it out to his ship, he is attacked by Troy.  He fights him alone and defeats him.  As Troy's ship sinks, Troy simply goes down with it.  As it does, he realizes he knew you.  He realized he could have dealt with you when you were very weak, but chose not too.

There is one more problem to deal with.  Fort El-Eal is falling and the shockwave is tearing their shipwave apart.  The Hero uses the Rune of Punishment one more time to save his people.

He succeeds, but at what cost?   Most of his compatriots believe he is dead.  He is even sent off in a funeral boat.  Due to the large army (108 Stars of Destiny), the Rune of Punishment has changed and will no longer hurt him.  The hero lives.  He works for the King of Obel after the war.

There is much more to this story that doesn't show up in the game itself.  This is just an overview.

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